Alignments for a candidate for asnB in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Desulfovibrio vulgaris Hildenborough

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate 209647 DVUA0073 asparagine synthase (glutamine-hydrolyzing), putative

Query= SwissProt::P64248
         (652 letters)



>MicrobesOnline__882:209647
          Length = 889

 Score =  167 bits (423), Expect = 2e-45
 Identities = 174/577 (30%), Positives = 249/577 (43%), Gaps = 78/577 (13%)

Query: 35  HRGPDE---------------SGTWHAVDGASGG-----VVFGFNRLSIIDIAH-SHQPL 73
           HRGPD                +G  H+ D  + G     V  G  RLSI+D++  S QPL
Sbjct: 29  HRGPDAGYGVSFRRQSTGAFAAGRRHSADALAAGLEPAPVWLGHRRLSILDLSDKSAQPL 88

Query: 74  RWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAVFATDGDGEAILAGYHHWGTEVLQR 133
           R G         +VFNGE++NY+ELR EL T  G  F T GD E +LA Y HWG   L+R
Sbjct: 89  RRGDLH------IVFNGELFNYIELRSEL-TALGEHFETSGDTEVLLASYRHWGAGCLER 141

Query: 134 LRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAV-------ASEKKCL-LDLVE 185
             G+FAFA++D     LF ARDPFG+KP          AV       ASE K +    + 
Sbjct: 142 FNGIFAFAIFDASRGSLFAARDPFGVKPFHYGVKPFHYAVTHDFLIFASEIKAISASGLV 201

Query: 186 LVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVITRYFVPRF 245
           L  +D ++    L +   L   P+  T    +R++  G    + +    P +TRY+ PR 
Sbjct: 202 LRKWDPDVASAYLSY--ALTTAPQGRTFFENIRQIPPGHCLTLASPDDEPSVTRYYAPRI 259

Query: 246 AASPITNDNDQARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAALAIRHN--PR 303
             +P    +     DE   ++  S    MR+D  VG  LS GIDS  +AA  +     P 
Sbjct: 260 TETP---RSLHELVDEGAGLIRQSCRIRMRSDRDVGLCLSSGIDSANVAAALVAEGIAPE 316

Query: 304 LITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSADEFVAALPEIVWYL---DEPVAD 360
             +           E  +  A A+ +G  H+  +   D    A  +IV Y+   DEP   
Sbjct: 317 CYSIDAA-SSSMLDEFPLITALADKLGL-HVNPIRHPDAIPTA--DIVRYMLFNDEPSLF 372

Query: 361 PALVPLFFVAREARK-HVKVVLSGEGADELFGGYTIYREPLSLRPFDYLPKPLRRSMGKV 419
                 F + RE RK  V V +SG G DELF GY  Y  P  +R  D L +  RR M  +
Sbjct: 373 WGSYNQFHLYREMRKLGVIVSMSGHGGDELFCGYQRY-YPAVVR--DMLAQ--RRIMSLI 427

Query: 420 SKPLPEGMRGKSLLHRGSLTLEERYYGN--------ARSFSGAQLREVLPGFRPDWTHTD 471
              L +      +  R ++      Y +        A   +   L+  +     +W  T 
Sbjct: 428 WWCLRQSRH--LMQDRRTIRSTWDSYSHPLGWANDYAHDIAALHLKHTIAD-PEEWISTF 484

Query: 472 VTAPVYAESAGWDPVARMQHIDLFTWLRGDILVKADKITMANSLELRVPFLDPEVFAVAS 531
           V A  + E          Q   LFT+    +L  AD+ +MA+ +E RVP LD  ++   +
Sbjct: 485 VGASSWGE---------QQQKSLFTYELQYLLRDADRNSMAHGIEERVPLLDTRLYEFCA 535

Query: 532 RLPAGAKITRTTTKYALRRALEPIVPAHV-LHRPKLG 567
            +P    + +      L R L P +P  +  H+ K G
Sbjct: 536 SVPL-KDLCQDGYLKGLARQLFPAIPESLRFHQIKRG 571


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: 1485
Number of extensions: 88
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 652
Length of database: 889
Length adjustment: 40
Effective length of query: 612
Effective length of database: 849
Effective search space:   519588
Effective search space used:   519588
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: 55 (25.8 bits)

Align candidate 209647 DVUA0073 (asparagine synthase (glutamine-hydrolyzing), putative)
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.7713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.4e-108  347.9   0.0   4.9e-107  344.9   0.0    1.9  1  lcl|MicrobesOnline__882:209647  DVUA0073 asparagine synthase (gl


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:209647  DVUA0073 asparagine synthase (glutamine-hydrolyzing), putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.9   0.0  4.9e-107  4.9e-107       1     509 [.       2     563 ..       2     571 .. 0.84

  Alignments for each domain:
  == domain 1  score: 344.9 bits;  conditional E-value: 4.9e-107
                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkd........................ekeenailghrRLai 55 
                                     Cgiagi+ +k+ +++ ++ +++ml  ++hRGPDa                               + + + lghrRL+i
  lcl|MicrobesOnline__882:209647   2 CGIAGIISRKDRNVS-SQPLNRMLTSQEHRGPDAGY--GVsfrrqstgafaagrrhsadalaagLEPAPVWLGHRRLSI 77 
                                     *********998666.59***************862..2235679****************98626789********** PP

                       TIGR01536  56 idlseg.aQPlsnekevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekk 133
                                      dls++ aQPl+  +   ivfnGE++N+ eLr el + G +Fet  DtEV+La+y++wg  ++er++G FAfa++d+++
  lcl|MicrobesOnline__882:209647  78 LDLSDKsAQPLRRGD-LHIVFNGELFNYIELRSELTALGEHFETSGDTEVLLASYRHWGAGCLERFNGIFAFAIFDASR 155
                                     *****99*****999.68************************************************************* PP

                       TIGR01536 134 gelflaRDrlGikPLY.......yaseqgkllfaSEiKallalkeikaeldkealaelltlq..lvptektlfkevkel 203
                                     g lf+aRD++G+kP++       ya +++ l+faSEiKa+ a   + ++ d ++++ +l++   + p+++t+f++++++
  lcl|MicrobesOnline__882:209647 156 GSLFAARDPFGVKPFHygvkpfhYAVTHDFLIFASEIKAISASGLVLRKWDPDVASAYLSYAltTAPQGRTFFENIRQI 234
                                     **********9877651111111667799***************9999999999999999887678999********** PP

                       TIGR01536 204 epakal.....dgeekleeywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak 277
                                     +p+++l     d+e ++ +y+  + +e+  s++elv+e   l++++ + r+++d+ vg++lS+G+DS  vaa + +e  
  lcl|MicrobesOnline__882:209647 235 PPGHCLtlaspDDEPSVTRYYAPRITETPRSLHELVDEGAGLIRQSCRIRMRSDRDVGLCLSSGIDSANVAAALVAEGI 313
                                     ******9998877788888***************************************************987655533 PP

                       TIGR01536 278 sevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvk 356
                                      + + +si+ + s+ lde   + ++ad+lg++ + +    +   +++ + +l  +ep  +  s+ +++l +++r+ gv 
  lcl|MicrobesOnline__882:209647 314 -APECYSIDAASSSMLDEFPLITALADKLGLHVNPIRHPDAIPTADIVRYMLFNDEPSLFWGSYNQFHLYREMRKLGVI 391
                                     .359***************************99988877777788899999999************************* PP

                       TIGR01536 357 VvLsGeGaDElfgGYeyfreakaeeale..........lpeaselaekkl.............llqaklakeselkell 412
                                     V +sG G+DElf GY+++  a ++  l           + + s+     +                       ++   +
  lcl|MicrobesOnline__882:209647 392 VSMSGHGGDELFCGYQRYYPAVVRDMLAqrrimsliwwCLRQSR-----HlmqdrrtirstwdS--------YSHPLGW 457
                                     ******************99998888884555554333111122.....122222222332221........2222233 PP

                       TIGR01536 413 kakleeelkekeelkkelkee.........seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelals 481
                                       ++ ++++  + +++    e         s+  e +++ l ++  ++l+++ Dr smah++E RvP+lD +l e+++s
  lcl|MicrobesOnline__882:209647 458 ANDYAHDIAALHLKHTIADPEewistfvgaSSWGEQQQKSLFTYELQYLLRDaDRNSMAHGIEERVPLLDTRLYEFCAS 536
                                     33444444444333333322245566666699999999999999999999999************************** PP

                       TIGR01536 482 ippelklrdgkeKvlLreaaeellPeei 509
                                     +p +  ++dg  K l r+++ + +Pe++
  lcl|MicrobesOnline__882:209647 537 VPLKDLCQDGYLKGLARQLFPA-IPESL 563
                                     ******************9964.56665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (889 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 5.19
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
the source code
instructions for running GapMind on your computer
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