Alignments for a candidate for argH in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Teredinibacter turnerae T7901

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_015817126.1 TERTU_RS00855 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_000023025.1:WP_015817126.1
          Length = 465

 Score =  448 bits (1152), Expect = e-130
 Identities = 229/454 (50%), Positives = 308/454 (67%)

Query: 7   KLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAG 66
           K WGGRF      +VE F AS++FDQ+L   D+ GSIAH TML   G++S ++   I  G
Sbjct: 9   KPWGGRFSEATDAFVERFTASVNFDQRLYHHDINGSIAHATMLASVGVLSDDEKNAIIEG 68

Query: 67  LEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLK 126
           LE + ++ ++G   + VS ED+HMN+E+ LT +IG    KLHT RSRNDQVATD+ LYL+
Sbjct: 69  LEGIRKDIESGAFTWSVSLEDVHMNIEAELTKRIGITGKKLHTGRSRNDQVATDIRLYLR 128

Query: 127 AKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSER 186
            ++D + ++L  L+  L+ LA++  HTIMPG+THLQ AQP++FGHHL+A+Y M +RD  R
Sbjct: 129 DEIDVIGKELTRLQQGLLFLAEREAHTIMPGFTHLQTAQPVTFGHHLLAWYEMLSRDYGR 188

Query: 187 FIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNA 246
            +   K  + SPLGAAALAGTT+PIDRE TA L+GF  P  NSLD+VSDRDF +EF + A
Sbjct: 189 LMGCRKRLNQSPLGAAALAGTTYPIDREQTAALLGFNHPTRNSLDSVSDRDFAIEFSAFA 248

Query: 247 SILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYAN 306
           ++LM H+SR  EE++ W S ++ F+ L D F TGSSIMPQKKNPD+ EL+RGK+GRV  +
Sbjct: 249 ALLMTHLSRASEELVLWTSAQFNFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRVNGH 308

Query: 307 LFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQK 366
           L  LLT+MK+ PLAYNKD QEDKE +FDT +T+   L   A M+ ++  N   M E+ ++
Sbjct: 309 LIALLTLMKSQPLAYNKDNQEDKEPLFDTVDTVKDCLRAFADMVPALNANKAAMLEAAKR 368

Query: 367 DFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVY 426
            FS AT+LADYL  KG+PFR +HEIVGK +         L ++ L   Q  SD+IE DV+
Sbjct: 369 GFSTATDLADYLVRKGIPFRDSHEIVGKSVAFGIAQNKDLSEMTLAELQQFSDVIENDVF 428

Query: 427 ETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
           + L    +V  R  +GGT   QV   +  AK+ L
Sbjct: 429 DVLTLEGSVAARDHIGGTAPAQVLKAVELAKEEL 462


Lambda     K      H
   0.318    0.132    0.378 

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: 582
Number of extensions: 24
Number of successful extensions: 1
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: 460
Length of database: 465
Length adjustment: 33
Effective length of query: 427
Effective length of database: 432
Effective search space:   184464
Effective search space used:   184464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_015817126.1 TERTU_RS00855 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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/TIGR00838.hmm
# target sequence database:        /tmp/gapView.12326.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-197  642.3   0.0   2.8e-197  642.1   0.0    1.0  1  lcl|NCBI__GCF_000023025.1:WP_015817126.1  TERTU_RS00855 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015817126.1  TERTU_RS00855 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.1   0.0  2.8e-197  2.8e-197       2     454 ..      11     462 ..      10     463 .. 1.00

  Alignments for each domain:
  == domain 1  score: 642.1 bits;  conditional E-value: 2.8e-197
                                 TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg 70 
                                               wggR+++++d  v++f+as++fD++l+++Di+gsiah+++La +g+l+++e++ +ie+Le +++++++g
  lcl|NCBI__GCF_000023025.1:WP_015817126.1  11 WGGRFSEATDAFVERFTASVNFDQRLYHHDINGSIAHATMLASVGVLSDDEKNAIIEGLEGIRKDIESG 79 
                                               9******************************************************************** PP

                                 TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalve 139
                                               +++++v+ eD+H+++E+el++++g   gkklhtgrsRnDqvatd+rlylrd+++ + ++l  l++ l+ 
  lcl|NCBI__GCF_000023025.1:WP_015817126.1  80 AFTWSVSLEDVHMNIEAELTKRIG-ITGKKLHTGRSRNDQVATDIRLYLRDEIDVIGKELTRLQQGLLF 147
                                               ************************.999***************************************** PP

                                 TIGR00838 140 kAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidre 208
                                               +Ae+e +t+mpg+tHLq AqP+t++Hhlla+ eml+rD+ Rl+   kR+n+sPlG++Alagt+++idre
  lcl|NCBI__GCF_000023025.1:WP_015817126.1 148 LAEREAHTIMPGFTHLQTAQPVTFGHHLLAWYEMLSRDYGRLMGCRKRLNQSPLGAAALAGTTYPIDRE 216
                                               ********************************************************************* PP

                                 TIGR00838 209 llaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssi 277
                                               ++a+lLgF++ ++nsld+vsdRDf+iE+ + aallm+hlsr +Eel+l++s+ f+f++l+d++++gssi
  lcl|NCBI__GCF_000023025.1:WP_015817126.1 217 QTAALLGFNHPTRNSLDSVSDRDFAIEFSAFAALLMTHLSRASEELVLWTSAQFNFIDLPDRFCTGSSI 285
                                               ********************************************************************* PP

                                 TIGR00838 278 mPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllke 346
                                               mPqKKnpDv El+Rgktgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++tv+++l++++ ++  
  lcl|NCBI__GCF_000023025.1:WP_015817126.1 286 MPQKKNPDVPELVRGKTGRVNGHLIALLTLMKSQPLAYNKDNQEDKEPLFDTVDTVKDCLRAFADMVPA 354
                                               ********************************************************************* PP

                                 TIGR00838 347 lkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekl 415
                                               l+ nk  + eaak++f++atdlAdylvrkG+PFR++heivG+ va  i++ k+l+e+tl+elq++s  +
  lcl|NCBI__GCF_000023025.1:WP_015817126.1 355 LNANKAAMLEAAKRGFSTATDLADYLVRKGIPFRDSHEIVGKSVAFGIAQNKDLSEMTLAELQQFSDVI 423
                                               ********************************************************************* PP

                                 TIGR00838 416 eedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               e+dv++vl+le +v++rd +GGta+++v ka+e ak+el
  lcl|NCBI__GCF_000023025.1:WP_015817126.1 424 ENDVFDVLTLEGSVAARDHIGGTAPAQVLKAVELAKEEL 462
                                               ************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (465 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.01
//
[ok]

This GapMind analysis is from Apr 10 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