Alignments for a candidate for argH in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Chlorobium phaeobacteroides BS1

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_012474743.1 CPHAMN1_RS06570 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_000020545.1:WP_012474743.1
          Length = 466

 Score =  441 bits (1134), Expect = e-128
 Identities = 224/459 (48%), Positives = 309/459 (67%)

Query: 2   TTKNHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAA 61
           +T    LW  RF     +    F +S+  D+ L + D+KGSIAHVTML E+ II  E+A 
Sbjct: 6   STGKELLWQSRFSEPFDREALLFSSSVDVDKVLYQEDIKGSIAHVTMLSEEAIIPVEEAR 65

Query: 62  TIKAGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDM 121
            I  GLED+ +E  +G L  D  +EDIH  +E+ L  KIGP+AGK+H+ RSRNDQVATD 
Sbjct: 66  LIIEGLEDIEQEISSGALIPDWEDEDIHTVIENRLKEKIGPIAGKMHSGRSRNDQVATDT 125

Query: 122 HLYLKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFT 181
            LYLK  + E+ E L  L+T+LV+ AD + +TI+ GYTHLQ AQP+S GH+ +AY+NMF 
Sbjct: 126 RLYLKKVIGELGEALDGLKTLLVEKADIYRNTIIFGYTHLQRAQPVSAGHYYLAYFNMFL 185

Query: 182 RDSERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILE 241
           RD ER     K  D+SPLGAAA AG+T PI+ + + +L+ F++ + NS DAVSDRD I+E
Sbjct: 186 RDGERLKDLFKRVDISPLGAAAFAGSTLPINAKRSMELLDFSDLFQNSTDAVSDRDIIIE 245

Query: 242 FLSNASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSG 301
           F+S  SI+MMH+SR CE++I W S E+ ++ +SD FSTGSSIMPQKKN D+AEL+RGK+G
Sbjct: 246 FISACSIIMMHLSRFCEDLILWSSSEFNYIEISDAFSTGSSIMPQKKNADIAELVRGKTG 305

Query: 302 RVYANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMA 361
           RVY NL  +LT+MK+LPL+YN+D+QEDK  +FD+A +   ++ I   ML+   +N+K + 
Sbjct: 306 RVYGNLMSILTIMKSLPLSYNRDMQEDKPPLFDSAGSTVSSVRIFTKMLAHTRLNEKRLK 365

Query: 362 ESTQKDFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLI 421
             T +D S ATE+A+YL  K +PFR+AH I GK++    +    L  + LE Y+   DL 
Sbjct: 366 TLTGEDLSLATEIAEYLVRKNLPFREAHRITGKIVSHAIEKRTSLPKISLEEYRGFCDLF 425

Query: 422 EEDVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
            ED+Y+ L    ++  +HS G T F  V+ QI  A+  L
Sbjct: 426 NEDLYDALTPEASINSKHSHGSTSFASVEQQITIARGKL 464


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: 576
Number of extensions: 17
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: 466
Length adjustment: 33
Effective length of query: 427
Effective length of database: 433
Effective search space:   184891
Effective search space used:   184891
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_012474743.1 CPHAMN1_RS06570 (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.7316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-179  581.9   0.0   6.1e-179  581.7   0.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474743.1  CPHAMN1_RS06570 argininosuccinat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474743.1  CPHAMN1_RS06570 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.7   0.0  6.1e-179  6.1e-179       1     454 [.      12     464 ..      12     465 .. 0.99

  Alignments for each domain:
  == domain 1  score: 581.7 bits;  conditional E-value: 6.1e-179
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               lw++R+++  d ++  f++s++ Dk l+++Di+gsiah+++L ++ i+  eea+ +ie+Le++++e+++
  lcl|NCBI__GCF_000020545.1:WP_012474743.1  12 LWQSRFSEPFDREALLFSSSVDVDKVLYQEDIKGSIAHVTMLSEEAIIPVEEARLIIEGLEDIEQEISS 80 
                                               7******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g+l +++++eDiH+++E++l +k+g  +++k+h+grsRnDqvatd rlyl++ + el eal  l++ lv
  lcl|NCBI__GCF_000020545.1:WP_012474743.1  81 GALIPDWEDEDIHTVIENRLKEKIG-PIAGKMHSGRSRNDQVATDTRLYLKKVIGELGEALDGLKTLLV 148
                                               *************************.9999*************************************** PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               ekA+   +t++ gytHLqrAqP++ +H+ lay++m+ rD eRl+d +kRv+ sPlG++A+ag++++i+ 
  lcl|NCBI__GCF_000020545.1:WP_012474743.1 149 EKADIYRNTIIFGYTHLQRAQPVSAGHYYLAYFNMFLRDGERLKDLFKRVDISPLGAAAFAGSTLPINA 217
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               +++ elL F+++ +ns davsdRD iiE++sa++++m+hlsr++E+lil+ss+Ef+++e+sd++s+gss
  lcl|NCBI__GCF_000020545.1:WP_012474743.1 218 KRSMELLDFSDLFQNSTDAVSDRDIIIEFISACSIIMMHLSRFCEDLILWSSSEFNYIEISDAFSTGSS 286
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKn+D+aEl+Rgktgrv+Gnl+++lti+K+lPl+Yn+D+qEdk++lfd+   + ++++++t +l+
  lcl|NCBI__GCF_000020545.1:WP_012474743.1 287 IMPQKKNADIAELVRGKTGRVYGNLMSILTIMKSLPLSYNRDMQEDKPPLFDSAGSTVSSVRIFTKMLA 355
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                               + ++n++rl+ ++ ++ +lat++A+ylvrk +PFReah+i+G++v +aiek ++l +++lee++ +   
  lcl|NCBI__GCF_000020545.1:WP_012474743.1 356 HTRLNEKRLKTLTGEDLSLATEIAEYLVRKNLPFREAHRITGKIVSHAIEKRTSLPKISLEEYRGFCDL 424
                                               ********************************************************************* PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               ++ed++++l++e +++ ++++G t++++ve++i  a+ +l
  lcl|NCBI__GCF_000020545.1:WP_012474743.1 425 FNEDLYDALTPEASINSKHSHGSTSFASVEQQITIARGKL 464
                                               *********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (466 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: 8.63
//
[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