Alignments for a candidate for asnB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Sphingomonas koreensis DSMZ 15582

Align Putative asparagine synthetase [glutamine-hydrolyzing]; EC 6.3.5.4 (characterized)
to candidate Ga0059261_3121 Ga0059261_3121 asparagine synthase (glutamine-hydrolyzing)

Query= SwissProt::P64248
         (652 letters)



>FitnessBrowser__Korea:Ga0059261_3121
          Length = 631

 Score =  255 bits (652), Expect = 4e-72
 Identities = 205/661 (31%), Positives = 308/661 (46%), Gaps = 80/661 (12%)

Query: 1   MCGLLAFVAAPAGAAGPEGADAASAIARASHLMRHRGPDESGTWHAVDGASGGVVFGFNR 60
           MCG++A  A  A            ++     ++ HRGPD+ G+ H  DG  G    G NR
Sbjct: 1   MCGIVAISAPDA---------RRFSLDATLDVIAHRGPDDRGS-HVSDG--GDAALGQNR 48

Query: 61  LSIIDIAHS-HQPLRWGPPEAPDRYVLVFNGEIYNYLELRDELRTQHGAV-FATDGDGEA 118
           LSIID++ + HQP+ W   +   RYV+ +NGE YN+  LR EL  +HGA+ +    D E 
Sbjct: 49  LSIIDLSCAGHQPM-W---DHSRRYVISYNGETYNFAALRAELEARHGAIPWTGSSDTEV 104

Query: 119 ILAGYHHWGTEVLQRLRGMFAFALWDTVTRELFCARDPFGIKPLFIATGAGGTAVASEKK 178
           ++ G+   G   L +L G+FA A++DT  + +   RDP GIKPL      GG    SE K
Sbjct: 105 VIEGFAREGIPFLDKLNGIFALAIYDTADQVMHVLRDPLGIKPLVATEQHGGIFFCSEIK 164

Query: 179 CLLDLVELVGFDTEIDHRALQHYTVLQYVPEPETLHRGVRRLESGCFARIRADQLAPVIT 238
            LL L  L      +   +L       YVPEP TL+    ++E G     RA +L    T
Sbjct: 165 GLLTLPAL---QRTLRRESLAEQLAFMYVPEPHTLYHEFHKVEPGVCFTYRAGKLL-ART 220

Query: 239 RYFVPRFAASPITNDND--QARYDEITAVLEDSVAKHMRADVTVGAFLSGGIDSTAIAAL 296
             F     A PIT + +  +A     TA ++  V     ADV V  FLSGG+DS+A+A  
Sbjct: 221 PLFAWLNNAQPITGEAEAIEALRHAFTAAVDRQVV----ADVPVSLFLSGGLDSSAVADQ 276

Query: 297 AIR-----HNPRLITFTTGFEREGFSEIDVAVASAEAIGARHIAKVVSAD-EFVAALPEI 350
           A+R     H+   I F+           D+  A   A       KV+ AD +F++ LP++
Sbjct: 277 AVRSGASIHDAYTIAFSDADRSLDAQSDDLHYAQIMADRLGIDLKVIEADSDFLSMLPDL 336

Query: 351 VWYLDEPVADPALVPLFFVAREARKH-VKVVLSGEGADELFGGYTIYREPLSLRPFDYLP 409
             ++++  +DPA +  + +   ARK  +KV+LSG+GADE  GGY  Y    + R    +P
Sbjct: 337 AGFMEDGFSDPAAINTWLICAGARKQGIKVMLSGQGADEFLGGYRRY---FAERALQRMP 393

Query: 410 KPLRRSMGKVSKPLPEGMRGK-SLLHR------------------------GSLTLEERY 444
             +R ++   S  LP  + GK + L+R                           T+   +
Sbjct: 394 GFVRSALSATSGMLPANLPGKFNALNRRFKRFANLAAQPPRDRILGMYSWATPATIGGLF 453

Query: 445 YGNARSFSGAQLREVLPGFRPDWTHTDVTAPVYAESAGWDPVARMQHIDLFTWLRGDILV 504
                S  G Q + +L G  P                  D V  +  ID    L    L 
Sbjct: 454 AAPLASHPGEQFQALLDGLPPG-----------------DCVDTLMAIDRQYDLLSLNLT 496

Query: 505 KADKITMANSLELRVPFLDPEVFAVASRLPAGAKITRTTTKYALRRALEPIVPAHVLHRP 564
             D+++MA  +E RVPFLD ++  V + +PA  K+     KY  ++A+EP +P  +++R 
Sbjct: 497 YTDRMSMAVGVEARVPFLDFDLVRVMNAIPASLKVKGRQGKYIFKKAMEPQLPHEIIYRS 556

Query: 565 KLGFPVPIRHWLRAGELLEWAYATVGSSQAGHLVDIAAVYRMLDEHRCGSSDHSRRLWTM 624
           K GF +PIR W+     L   Y      +A  + +  A+ R+  E   G++DH+  L T+
Sbjct: 557 KAGFGLPIRAWMDKRNDLLNRYLNRARIEAQGIFNADAIERIRGEQAAGAADHANTLLTL 616

Query: 625 L 625
           L
Sbjct: 617 L 617


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: 916
Number of extensions: 46
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 652
Length of database: 631
Length adjustment: 38
Effective length of query: 614
Effective length of database: 593
Effective search space:   364102
Effective search space used:   364102
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 Ga0059261_3121 Ga0059261_3121 (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.3520409.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-119  386.4   0.0   2.1e-119  385.8   0.0    1.3  1  FitnessBrowser__Korea:Ga0059261_3121  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Korea:Ga0059261_3121  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.8   0.0  2.1e-119  2.1e-119       1     517 []       2     560 ..       2     560 .. 0.86

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 2.1e-119
                             TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.ev 71 
                                           Cgi++i + +a     +  +++ l+++ahRGPD++g + + +  +a+lg++RL+iidls + +QP+ +++ ++
  FitnessBrowser__Korea:Ga0059261_3121   2 CGIVAISAPDAR----RFSLDATLDVIAHRGPDDRGSHVS-DGGDAALGQNRLSIIDLSCAgHQPMWDHSrRY 69 
                                           888888888664....566888899***********9888.89****************888*********** PP

                             TIGR01536  72 vivfnGEIYNheeLreeleek.G.yeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDr 142
                                           vi +nGE YN+ +Lr+ele++ G + +++ sDtEV+++ +   g  ++++L+G FA+a++d++++ +++ RD+
  FitnessBrowser__Korea:Ga0059261_3121  70 VISYNGETYNFAALRAELEARhGaIPWTGSSDTEVVIEGFAREGIPFLDKLNGIFALAIYDTADQVMHVLRDP 142
                                           *******************9833257999******************************************** PP

                             TIGR01536 143 lGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal..dgee 213
                                           lGikPL  ++++g ++f+SEiK+ll+l++ ++ l++e lae+l++ +vp+++tl++e +++ep+ ++  +  +
  FitnessBrowser__Korea:Ga0059261_3121 143 LGIKPLVATEQHGGIFFCSEIKGLLTLPALQRTLRRESLAEQLAFMYVPEPHTLYHEFHKVEPGVCFtyRAGK 215
                                           *******************************************************************973333 PP

                             TIGR01536 214 klee...ywevekeevkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktF 283
                                            l++   +  +++ +  + e e++e lr+++++av++++vadvpv ++lSGGlDSs+va  a +  +s    +
  FitnessBrowser__Korea:Ga0059261_3121 216 LLARtplFAWLNNAQPITGEAEAIEALRHAFTAAVDRQVVADVPVSLFLSGGLDSSAVADQAVRSGASIHDAY 288
                                           333367754445555555578899***********************************9999998866679* PP

                             TIGR01536 284 sigfe.dskdldesk....aarkvadelgtehkevliseeevlkeleevilaleeptairasiplyllsklar 351
                                           +i+f   + +ld+++    +a+ +ad lg+++k ++ +  ++l+ l+++   +e+ ++++a+i ++l++  ar
  FitnessBrowser__Korea:Ga0059261_3121 289 TIAFSdADRSLDAQSddlhYAQIMADRLGIDLKVIEAD-SDFLSMLPDLAGFMEDGFSDPAAINTWLICAGAR 360
                                           *****54555554437888*************999976.589******************************* PP

                             TIGR01536 352 ekgvkVvLsGeGaDElfgGYeyfreakaeeale............................lpeaselaekkl 396
                                           ++g+kV+LsG+GaDE +gGY +++   a +++                             +          +
  FitnessBrowser__Korea:Ga0059261_3121 361 KQGIKVMLSGQGADEFLGGYRRYFAERALQRMPgfvrsalsatsgmlpanlpgkfnalnrrF----------K 423
                                           *************************9999988888888888877777777655554444441..........0 PP

                             TIGR01536 397 ..............llqaklakeselkellkakleeel.kekeelkkelkeeseleellrldle.lllsdllr 453
                                                         l   ++a+  +   l+ a l ++  +++++l + l+    ++ l+  d +  lls +l 
  FitnessBrowser__Korea:Ga0059261_3121 424 rfanlaaqpprdriLGMYSWATPATIGGLFAAPLASHPgEQFQALLDGLPPGDCVDTLMAIDRQyDLLSLNLT 496
                                           3333344444454477778888888888888877766513444555556666888888777765268899999 PP

                             TIGR01536 454 akDrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                             Dr+sma ++E+RvPflD +lv+++  ip++lk++  + K+++++a+e  lP+ei +R+K++f
  FitnessBrowser__Korea:Ga0059261_3121 497 YTDRMSMAVGVEARVPFLDFDLVRVMNAIPASLKVKGRQGKYIFKKAMEPQLPHEIIYRSKAGF 560
                                           99************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (631 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.05
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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