Alignments for a candidate for asnB in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Shewanella loihica PV-4

Align asparagine synthase (glutamine-hydrolysing) 3; EC 6.3.5.4 (characterized)
to candidate 5210610 Shew_3038 asparagine synthase (glutamine-hydrolyzing) (RefSeq)

Query= CharProtDB::CH_007942
         (614 letters)



>FitnessBrowser__PV4:5210610
          Length = 590

 Score =  252 bits (644), Expect = 3e-71
 Identities = 176/554 (31%), Positives = 273/554 (49%), Gaps = 56/554 (10%)

Query: 1   MCGITGWVDFKKQLVQEKQTMDRMTDTLSKRGPDDSNVWGEHHVLFGHKRLAVVDI-EGG 59
           MCGI G + F      ++  +  M D L+ RGPD   ++       GH+RL ++D+ E G
Sbjct: 1   MCGIAGELSFTTSAKVDQ--VAAMLDKLAPRGPDGQGLYSLGPCCLGHRRLKIIDLSEHG 58

Query: 60  RQPMACTYKGDTYTIIYNGELYNTEDLRKELRARGHQFERTSDTEVLLHSYIEWQEDCVD 119
            QPM     G   T+++NG +YN   LR EL   G+ F   SD+EV+L +Y  W   CV+
Sbjct: 59  AQPMVDAELG--LTLVFNGCIYNYRALRAELSELGYHFFSHSDSEVILKAYAHWGRQCVE 116

Query: 120 HLNGIFAFAVWDEKRNLLFAARDRLGVKPFFYTKEGSSFLFGSEIKAILAHPDIKARVDR 179
             NG+FAFA+ +     LF ARDRLG+KP +Y K+G S +F S + A+L HP     +D 
Sbjct: 117 KFNGMFAFAIHERDTGRLFIARDRLGIKPLYYFKDGHSLVFASSLPALLRHPVADTEIDP 176

Query: 180 TGLSEIFGLGPSRTPGTGIFKGIKEIRPAHALTFSKDG-LNIWRYWNVE--SEKHTDSFD 236
             L+            T +FK I ++  AH +    DG ++   YW++   S   T++ +
Sbjct: 177 QSLNHYLCFRAIVGDKT-LFKQIHKLEAAHWMLVRPDGQVDHQSYWHLSPGSSLETETEE 235

Query: 237 DTVANVRSLFQDAVTRQLVSDVPVCTFLSGGLDSSAITAIAAGHFEKEGKAPLHTYSIDY 296
                +     D+  R+L +DVPV   LSGGLDSS I     G   + G+  +HT+SI +
Sbjct: 236 TWSQQLEQKLFDSAKRRLEADVPVGVLLSGGLDSSLI----VGLLHELGQKEIHTFSIGF 291

Query: 297 EENDKYFQASAFQPNDDGPWIEKMTEAFGTTHHKCVISQKDLVDHLEEAVLVKDLPGMAD 356
           ++        A +  ++  + + + E + T H K V+S  +L+ HL + V+    P ++ 
Sbjct: 292 DD-------VADEQGNEFKYSDLIAEHYQTRHQKIVVSHSELISHLPDCVMAMSEPMVSH 344

Query: 357 VDSSLLWFCREIKKDFVVSLSGECADEIFGGYPWFHTADVESGFPWMRST-EERIKLLSD 415
                    + + +   V  SG+ ADE+FGGY W+         P + +T E+  +   D
Sbjct: 345 DVIGFYLLSKTVSQHVKVVQSGQGADEVFGGYHWYP--------PMVDATAEDEAQTYQD 396

Query: 416 ---SWQKKLNLKEYVNAKYEETLAETPLLDGETGVDKARRQLFYLN---------MLWFM 463
              SWQ           +Y++ +AE PLLDG+   D  RR   +           ML   
Sbjct: 397 AYFSWQ---------YPEYQQLVAE-PLLDGDHAGDYVRRYFAHCPAETAIDKTLMLDTR 446

Query: 464 TNLLD----RKDRMSMGASLEVRVPFADHRLVEYVWNIPWEMKMHDNREKGILRKALEGI 519
             L+D    R D M+M   LE RVPF DH LVE    IP+++K+ +   K +L++    I
Sbjct: 447 VMLVDDPVKRVDNMTMAFGLEARVPFLDHELVELASRIPFDLKLKEG-GKYLLKQVARRI 505

Query: 520 LPDDILYRKKSPYP 533
           +P  ++ R K  +P
Sbjct: 506 IPHQVIDRPKGYFP 519


Lambda     K      H
   0.320    0.137    0.425 

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: 912
Number of extensions: 49
Number of successful extensions: 7
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: 614
Length of database: 590
Length adjustment: 37
Effective length of query: 577
Effective length of database: 553
Effective search space:   319081
Effective search space used:   319081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 5210610 Shew_3038 (asparagine synthase (glutamine-hydrolyzing) (RefSeq))
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.6410.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.7e-141  458.0   0.0   3.2e-141  457.8   0.0    1.0  1  lcl|FitnessBrowser__PV4:5210610  Shew_3038 asparagine synthase (g


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210610  Shew_3038 asparagine synthase (glutamine-hydrolyzing) (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.8   0.0  3.2e-141  3.2e-141       1     516 [.       2     517 ..       2     518 .. 0.90

  Alignments for each domain:
  == domain 1  score: 457.8 bits;  conditional E-value: 3.2e-141
                        TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsnek.evvivfn 76 
                                      Cgiag +  ++ ak   +++++ml++la RGPD++g+++      ++lghrRL iidlse  aQP+ +++   ++vfn
  lcl|FitnessBrowser__PV4:5210610   2 CGIAGELSFTTSAKV--DQVAAMLDKLAPRGPDGQGLYSL---GPCCLGHRRLKIIDLSEHgAQPMVDAElGLTLVFN 74 
                                      *********997776..79******************999...8***************998*********99***** PP

                        TIGR01536  77 GEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyaseq 154
                                      G IYN+++Lr+el e Gy+F ++sD+EViL+ay +wg+++ve+++GmFAfa++++ +g+lf+aRDrlGikPLYy +++
  lcl|FitnessBrowser__PV4:5210610  75 GCIYNYRALRAELSELGYHFFSHSDSEVILKAYAHWGRQCVEKFNGMFAFAIHERDTGRLFIARDRLGIKPLYYFKDG 152
                                      ****************************************************************************** PP

                        TIGR01536 155 gkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepakal....dgeekleeywevekee..v 226
                                       +l+faS + all+++ +++e+d + l ++l +   + +ktlfk++++le+a+ +    dg+ + ++yw+++  +   
  lcl|FitnessBrowser__PV4:5210610 153 HSLVFASSLPALLRHPVADTEIDPQSLNHYLCFRAIVGDKTLFKQIHKLEAAHWMlvrpDGQVDHQSYWHLSPGSslE 230
                                      **********************************889****************99997766666677**999777668 PP

                        TIGR01536 227 keseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeaksevktFsigfe..dskdldeskaarkv 302
                                      +e+ee+  ++l+++l d+ k+rl advpvgvllSGGlDSsl++ ++++  ++e++tFsigf+   +++ +e k+   +
  lcl|FitnessBrowser__PV4:5210610 231 TETEETWSQQLEQKLFDSAKRRLEADVPVGVLLSGGLDSSLIVGLLHELGQKEIHTFSIGFDdvADEQGNEFKYSDLI 308
                                      8999999******************************************************955567778889***** PP

                        TIGR01536 303 adelgtehkevliseeevlkeleevilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakae 380
                                      a++  t+h+++++s+ e++++l++ ++a+ ep+  +++i+ yllsk ++++ vkVv sG+GaDE+fgGY+++  +  +
  lcl|FitnessBrowser__PV4:5210610 309 AEHYQTRHQKIVVSHSELISHLPDCVMAMSEPMVSHDVIGFYLLSKTVSQH-VKVVQSGQGADEVFGGYHWYPPMVDA 385
                                      ***************************************************.********************986443 PP

                        TIGR01536 381 ealelpeaselaekklllqaklakeselkellkakleeelkekeelkkelkeeseleellrldlelllsdl.lrakDr 457
                                       a   ++    +++    + ++ + ++l      + +++  ++++ +++ ++e++++++l ld+  +l d+ +++ D 
  lcl|FitnessBrowser__PV4:5210610 386 TAEDEAQ----TYQDAYFSWQYPEYQQLVAEPLLDGDHAGDYVRRYFAHCPAETAIDKTLMLDTRVMLVDDpVKRVDN 459
                                      3333122....222222222222222222223334555666778888899999**********9998877626666** PP

                        TIGR01536 458 vsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeellPeeileRkKea 516
                                      ++ma +lE+RvPflD+elvela +ip +lkl++g  K+lL+++a++++P+++ +R+K  
  lcl|FitnessBrowser__PV4:5210610 460 MTMAFGLEARVPFLDHELVELASRIPFDLKLKEG-GKYLLKQVARRIIPHQVIDRPKGY 517
                                      *******************************987.7********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (590 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.36
//
[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