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

GapMind for catabolism of small carbon sources

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

Align Succinylglutamate desuccinylase; EC 3.5.1.96 (uncharacterized)
to candidate 5209453 Shew_1924 succinylglutamate desuccinylase (RefSeq)

Query= curated2:A4Y6M4
         (344 letters)



>FitnessBrowser__PV4:5209453
          Length = 355

 Score =  442 bits (1136), Expect = e-129
 Identities = 229/352 (65%), Positives = 263/352 (74%), Gaps = 17/352 (4%)

Query: 1   MLQALLDSKDFLALTLAHPEQFDGEFSFNLGDHTQVEVWDTGVIVFEPI---------QN 51
           M   L+ SKDFL LTL +P   +  F F LG HTQV VWDTGVI FEP+         + 
Sbjct: 1   MRDTLMLSKDFLQLTLDNPVGLEA-FEFTLGQHTQVSVWDTGVIQFEPLVTYEANQESEQ 59

Query: 52  EGKD-----IVLSCGVHGNETAPIELCNSLIKQLLQQKIIAKQRTLFLIGNPLAINNGTR 106
           +GK+     IVLS  VHGNETAPIELC+ LI  LL + +IA+ R LFLIGNP AI NGTR
Sbjct: 60  DGKEEALKSIVLSSAVHGNETAPIELCDQLITALLSETLIARHRLLFLIGNPPAILNGTR 119

Query: 107 IIDENMNRLFSGEHSNPPGLVNPERVRAKKLEAYVDRFFTAAADGRQRIHYDLHTAMRAS 166
            ++EN+NRLFSG H+   G  N ERVRAKKLE YVDRFF AA     R HYDLHTA+RAS
Sbjct: 120 FVEENLNRLFSGAHAK--GESNAERVRAKKLEQYVDRFFNAAPKDGSRYHYDLHTAIRAS 177

Query: 167 KHEKFAIYPYRPGRAFSGEQIMFLAASGVDTVLFHHEPTTTFSYFSSERYGADAFTIELG 226
           KHEKFAIYPY  G  +SGEQIMFLAA G++TVLFHHEPTTTFSYFS+  Y A AFTIELG
Sbjct: 178 KHEKFAIYPYPHGAPYSGEQIMFLAACGINTVLFHHEPTTTFSYFSAHGYQAHAFTIELG 237

Query: 227 KVYPMGQNDMTRFIATHEMFMRLITAKPLELDAFDADKVNLYQVCRVINKHFDDFEFTFA 286
           KV PMGQNDMTRFIA  EM  RL++ + LEL  FD  +VNLYQV R INK FDDF FTFA
Sbjct: 238 KVMPMGQNDMTRFIAVKEMLTRLVSGRDLELGEFDPSQVNLYQVHRSINKQFDDFSFTFA 297

Query: 287 TDVENFRSFPKGFVLAREGGQEIKVEHEFESVVFPNAKVPIGNRTVICLIPA 338
            DVENF +FP+G++LA++GG EIKVE E ES+VFPNA VP+G RTV+CL+PA
Sbjct: 298 DDVENFTAFPRGYILAKDGGTEIKVEAESESIVFPNANVPVGQRTVLCLVPA 349


Lambda     K      H
   0.323    0.139    0.412 

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: 455
Number of extensions: 12
Number of successful extensions: 4
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: 344
Length of database: 355
Length adjustment: 29
Effective length of query: 315
Effective length of database: 326
Effective search space:   102690
Effective search space used:   102690
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: 49 (23.5 bits)

Align candidate 5209453 Shew_1924 (succinylglutamate desuccinylase (RefSeq))
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

# 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.carbon/TIGR03242.hmm
# target sequence database:        /tmp/gapView.5521.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03242  [M=319]
Accession:   TIGR03242
Description: arg_catab_astE: succinylglutamate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.2e-113  363.8   0.1   4.8e-113  363.6   0.1    1.0  1  lcl|FitnessBrowser__PV4:5209453  Shew_1924 succinylglutamate desu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209453  Shew_1924 succinylglutamate desuccinylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.6   0.1  4.8e-113  4.8e-113       1     318 [.      10     346 ..      10     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 363.6 bits;  conditional E-value: 4.8e-113
                        TIGR03242   1 dflaltlekkepevtqge..aknvklrwldeGvlelePe..............aeaekslvisaGihGnetaPielle 62 
                                      dfl+ltl++  +    +    +  ++   d+Gv++ eP               +ea ks+v+s+ +hGnetaPiel +
  lcl|FitnessBrowser__PV4:5209453  10 DFLQLTLDNPVGLEAFEFtlGQHTQVSVWDTGVIQFEPLvtyeanqeseqdgkEEALKSIVLSSAVHGNETAPIELCD 87 
                                      79999999988844444413455566689*********************9999999********************* PP

                        TIGR03242  63 qllsdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagkasear 140
                                      ql++++++++l  ++rlL+++Gnp+a+ +g R++ee+lnRlf+G +++ e+  e+ Ra++Leq+v +ff+a+ +  +r
  lcl|FitnessBrowser__PV4:5209453  88 QLITALLSETLIARHRLLFLIGNPPAILNGTRFVEENLNRLFSGAHAKGESNAERVRAKKLEQYVDRFFNAAPKDGSR 165
                                      ***************************************************************************9** PP

                        TIGR03242 141 yhyDlhtaiRasklekfallPyq.ekpfdkellewlaaadldavllhkekggtfshfssekleaeactlelGkarPfG 217
                                      yhyDlhtaiRask+ekfa++Py  + p++ e++ +laa+++++vl+h+e+++tfs+fs++ ++a+a+t+elGk++P G
  lcl|FitnessBrowser__PV4:5209453 166 YHYDLHTAIRASKHEKFAIYPYPhGAPYSGEQIMFLAACGINTVLFHHEPTTTFSYFSAHGYQAHAFTIELGKVMPMG 243
                                      **********************98****************************************************** PP

                        TIGR03242 218 endlsqfqaitealralisdeaiparkke..elklfevvesilkksdsfelhvaedasnftefakGtllaedkderyr 293
                                      +nd+++f a++e l++l+s++ +   +++  +++l++v +si k+ d+f +  a+d++nft f++G++la+d  ++ +
  lcl|FitnessBrowser__PV4:5209453 244 QNDMTRFIAVKEMLTRLVSGRDLELGEFDpsQVNLYQVHRSINKQFDDFSFTFADDVENFTAFPRGYILAKDGGTEIK 321
                                      **********************99999987799********************************************* PP

                        TIGR03242 294 veeeeerilfPnakvanGlRaglll 318
                                      ve e+e+i+fPna+v  G+R +l l
  lcl|FitnessBrowser__PV4:5209453 322 VEAESESIVFPNANVPVGQRTVLCL 346
                                      **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (355 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: 00:00:00.01
# Mc/sec: 10.24
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources