Alignments for a candidate for asnB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Marinobacter adhaerens HP15

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate GFF4352 HP15_p187g60 asparagine synthase, glutamine-hydrolyzing

Query= SwissProt::P64248
         (652 letters)



>FitnessBrowser__Marino:GFF4352
          Length = 657

 Score =  323 bits (829), Expect = 1e-92
 Identities = 228/666 (34%), Positives = 334/666 (50%), Gaps = 54/666 (8%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG+        G  G E     SA+ + +  + HRGPD+SGTW  +   S G+ FG  R
Sbjct: 1   MCGITGIFG---GVPGSE--PLKSALKQMADAITHRGPDDSGTWEEL---SAGLGFGHRR 52

Query: 61  LSIIDIAHS-HQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQH--GAVFATDGDGE 117
           LSI+D++ + HQP+  G      R+VL FNGEIYN+  LR EL +     A +    D E
Sbjct: 53  LSIVDLSPAGHQPMLSGC----GRFVLAFNGEIYNHNALRRELESSGKVSAGWKGHSDTE 108

Query: 118 AILAGYHHWGTE-VLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASE 176
            +L  +  WG E  L+   GMFA ALWD   + L  ARD FG KPL+    AG    +SE
Sbjct: 109 TLLCAFTAWGVEKTLEMAAGMFAIALWDREEQSLTLARDRFGEKPLYYGLVAGALVFSSE 168

Query: 177 KKCLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFAR-----IRAD 231
            K L       G   E++   L+ Y     V   E++ + V +L +GC  +     IR  
Sbjct: 169 LKALQRAPRWRG---EVEPSVLESYLRFGCVGGQESIFKDVFKLPAGCLLKVSLLDIRHG 225

Query: 232 QLAPVITRYFVPRFAASPIT---NDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGI 288
           ++ PV+ R++ P  AA       N+N     D +   L  S+ + M ADV +GAFLSGG+
Sbjct: 226 EMPPVV-RWWSPVEAAGAALGGRNNNPDMALDNVEQALVASIRQQMAADVPLGAFLSGGV 284

Query: 289 DSTAIAALAIRHNPRLI-TFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAAL 347
           DS+ I AL      + + TF+ GF+   + E + A A A  +G  H     ++   +  +
Sbjct: 285 DSSLIGALMQSQTSQKVRTFSVGFDDPRYDESEHAAAVAAYLGTEHTTLRATSKMALDLV 344

Query: 348 PEIVWYLDEPVADPALVPLFFVAREARKHVKVVLSGEGADELFGGYTIYR-EPLSLRPFD 406
           P++    DEP AD + +P   ++   R+HV V LSG+  DELFGGY  Y   P       
Sbjct: 345 PKLPELYDEPFADSSQLPTCLISALTRQHVTVALSGDAGDELFGGYNRYVWVPRVWSKLS 404

Query: 407 YLPKPLRRSMGKVSKPLPEGMRGKSLLHRGSLTLEERY---------YGNARSFSGAQLR 457
            +P P+R+++G++ K +P   R   L+  G   L  RY         Y  A   + +  R
Sbjct: 405 RMPLPMRQTLGRMLKLVPSS-RYDRLMCLGRKVLPSRYQIRTFGEKLYKLADVLACSSDR 463

Query: 458 EVLPGF-----------RPDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKA 506
            +  G            R D+   +    +Y   AG+DPV  M  +D   ++  D+LVK 
Sbjct: 464 ALYGGLASMNRHPEQLLRTDYRSGNPVEDLYPALAGFDPVEWMMLMDTLNFMVDDVLVKV 523

Query: 507 DKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRPKL 566
           D+ +MA+SLE+R PFLDPEVF  A +LP   ++     K+ALR+ L   VP  ++ RPK+
Sbjct: 524 DRSSMASSLEVRAPFLDPEVFKAAWQLPLDMRVRNGEGKWALRQILYRHVPRELIERPKM 583

Query: 567 GFPVPIRHWLRAGELLEWAYATVGSSQAGHL--VDIAAVYRMLDEHRCGSSDHSRRLWTM 624
           GF +P+  WLR G L EWA   +G      +  +D  AV+ M D H  G   ++++LW +
Sbjct: 584 GFAIPLDDWLR-GPLREWAEDLLGVRWLSQIPALDAKAVHLMWDRHIQGQGHYAQQLWAV 642

Query: 625 LIFMLW 630
           L    W
Sbjct: 643 LQLSAW 648


Lambda     K      H
   0.323    0.138    0.428 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1138
Number of extensions: 61
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 652
Length of database: 657
Length adjustment: 38
Effective length of query: 614
Effective length of database: 619
Effective search space:   380066
Effective search space used:   380066
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)

Align candidate GFF4352 HP15_p187g60 (asparagine synthase, glutamine-hydrolyzing)
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01536.hmm
# target sequence database:        /tmp/gapView.496.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.1e-136  441.9   0.0   2.8e-136  441.5   0.0    1.2  1  lcl|FitnessBrowser__Marino:GFF4352  HP15_p187g60 asparagine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF4352  HP15_p187g60 asparagine synthase, glutamine-hydrolyzing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.5   0.0  2.8e-136  2.8e-136       1     517 []       2     585 ..       2     585 .. 0.86

  Alignments for each domain:
  == domain 1  score: 441.5 bits;  conditional E-value: 2.8e-136
                           TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evvi 73 
                                         Cgi+gi+     ++  ++a+k+m++++ hRGPD++g+w++  +++ ++ghrRL+i+dls + +QP+ +   + v+
  lcl|FitnessBrowser__Marino:GFF4352   2 CGITGIFGGVPGSEPLKSALKQMADAITHRGPDDSGTWEE-LSAGLGFGHRRLSIVDLSPAgHQPMLSGCgRFVL 75 
                                         *********998888779**********************.799***************998****99989**** PP

                           TIGR01536  74 vfnGEIYNheeLreeleekGy...eFetksDtEViLaayeewg.eelverLeGmFAfalwdekkgelflaRDrlG 144
                                          fnGEIYNh++Lr+ele  G     ++++sDtE +L+a+ +wg e+++e+ +GmFA+alwd++++ l laRDr+G
  lcl|FitnessBrowser__Marino:GFF4352  76 AFNGEIYNHNALRRELESSGKvsaGWKGHSDTETLLCAFTAWGvEKTLEMAAGMFAIALWDREEQSLTLARDRFG 150
                                         *******************9633369************************************************* PP

                           TIGR01536 145 ikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal.....dgeek 214
                                          kPLYy+  +g+l+f+SE+Kal ++++ + e++ ++l ++l +  v  ++++fk+v++l+++  l     d    
  lcl|FitnessBrowser__Marino:GFF4352 151 EKPLYYGLVAGALVFSSELKALQRAPRWRGEVEPSVLESYLRFGCVGGQESIFKDVFKLPAGCLLkvsllD---- 221
                                         ********************************************99****************999654441.... PP

                           TIGR01536 215 lee........ywevekee......vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakke 275
                                         +++        +w+  + +      ++++ + + ++++++l +++++++ advp+g++lSGG+DSsl+ a+++ +
  lcl|FitnessBrowser__Marino:GFF4352 222 IRHgemppvvrWWSPVEAAgaalggRNNNPDMALDNVEQALVASIRQQMAADVPLGAFLSGGVDSSLIGALMQSQ 296
                                         333455667779998888789999988999999****************************************** PP

                           TIGR01536 276 aksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllskla 350
                                           ++v+tFs+gf+ ++ +des++a++va++lgteh+++  +++ +l+ ++++    +ep+a++++ p+ l+s l+
  lcl|FitnessBrowser__Marino:GFF4352 297 TSQKVRTFSVGFD-DPRYDESEHAAAVAAYLGTEHTTLRATSKMALDLVPKLPELYDEPFADSSQLPTCLISALT 370
                                         *************.************************************************************* PP

                           TIGR01536 351 rekgvkVvLsGeGaDElfgGYeyfreakae..eale...............lpeaselaekkl............ 396
                                         r++ v+V+LsG+ +DElfgGY+++   ++   +  +               +                       
  lcl|FitnessBrowser__Marino:GFF4352 371 RQH-VTVALSGDAGDELFGGYNRYVWVPRVwsKLSRmplpmrqtlgrmlklV----------Pssrydrlmclgr 434
                                         ***.********************9875431044445555555555554440..........0444445555555 PP

                           TIGR01536 397 ..............................llqaklakeselkellkakleeelkekeelkkelkee........ 433
                                                                       l+  +   + + ++ll++++++++            +        
  lcl|FitnessBrowser__Marino:GFF4352 435 kvlpsryqirtfgeklykladvlacssdraLYGGLASMNRHPEQLLRTDYRSGNPVE---------Dlypalagf 500
                                         555665666666666665555555544442222233333334455555555544433.........144444556 PP

                           TIGR01536 434 seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPe 507
                                           +e ++  d+ +++ d++++k Dr sma slEvR+PflD e++++a+++p ++++r+g+ K+ Lr+++ +++P+
  lcl|FitnessBrowser__Marino:GFF4352 501 DPVEWMMLMDTLNFMVDDVLVKvDRSSMASSLEVRAPFLDPEVFKAAWQLPLDMRVRNGEGKWALRQILYRHVPR 575
                                         899************************************************************************ PP

                           TIGR01536 508 eileRkKeaf 517
                                         e+ eR+K++f
  lcl|FitnessBrowser__Marino:GFF4352 576 ELIERPKMGF 585
                                         ********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (657 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.86
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis