Alignments for a candidate for argG in Rhizobium etli CFN 42

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Rhizobium etli CFN 42

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate WP_011427116.1 RHE_RS20070 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>NCBI__GCF_000092045.1:WP_011427116.1
          Length = 407

 Score =  491 bits (1265), Expect = e-143
 Identities = 248/390 (63%), Positives = 298/390 (76%), Gaps = 3/390 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTSIILKWL+    AEV+ FTAD+GQGEE+E AR+KA   G  +    D+
Sbjct: 9   KVVLAYSGGLDTSIILKWLQTELGAEVVTFTADLGQGEELEPARKKAEMLGIKEIYIEDV 68

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRDFVFPM RA AVYEG YLLGTSIARPLI+KHL+ IA + GA+AIAHGATGKGND
Sbjct: 69  REEFVRDFVFPMFRANAVYEGVYLLGTSIARPLISKHLIDIARKTGADAIAHGATGKGND 128

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDANLL 179
           QVRFEL+AYAL PDIK+IAPWR+W+F+ R E++A+AE H IPV   +  E P+S+DANLL
Sbjct: 129 QVRFELSAYALNPDIKIIAPWRDWAFKSRTELLAFAEQHQIPVAKDKKGEAPFSVDANLL 188

Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239
           H S EG VLEDP  E P+ +   T  PE APD    ++V F +GD V++NG  +SPA LL
Sbjct: 189 HSSSEGKVLEDPAQEAPEYVHMRTISPEAAPDKATVIKVGFRKGDAVSINGVEMSPATLL 248

Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299
             LN  G  +G+GR+D+VENRFVGMKSRGVYETPGGTIL  A RA+ES+TLDR   H +D
Sbjct: 249 ATLNTYGRDNGIGRLDLVENRFVGMKSRGVYETPGGTILLSAHRAIESITLDRGAAHLKD 308

Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359
            + P+YAEL+YYGFW++PERE LQA  D     V G   LKLYKGNV V+GR++ KSLY 
Sbjct: 309 EIMPRYAELIYYGFWFSPEREMLQALIDKSQEYVEGEVTLKLYKGNVMVIGRESEKSLYS 368

Query: 360 QDLVSF-DEAGGYDQKDAEGFIKIQALRLR 388
             LV+F D+ G YDQKDA GFIK+ ALRLR
Sbjct: 369 DKLVTFEDDQGAYDQKDAAGFIKLNALRLR 398


Lambda     K      H
   0.319    0.137    0.402 

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: 502
Number of extensions: 15
Number of successful extensions: 3
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: 400
Length of database: 407
Length adjustment: 31
Effective length of query: 369
Effective length of database: 376
Effective search space:   138744
Effective search space used:   138744
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011427116.1 RHE_RS20070 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.15294.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-145  470.1   0.0   4.6e-145  469.8   0.0    1.0  1  lcl|NCBI__GCF_000092045.1:WP_011427116.1  RHE_RS20070 argininosuccinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092045.1:WP_011427116.1  RHE_RS20070 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.8   0.0  4.6e-145  4.6e-145       1     389 [.       9     400 ..       9     404 .. 0.97

  Alignments for each domain:
  == domain 1  score: 469.8 bits;  conditional E-value: 4.6e-145
                                 TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 
                                               kvvlaysGGlDts++lk+l+ + gaev+++t+d+Gq+ e+l+ +++ka  lG ++ y+ D reefv+d+
  lcl|NCBI__GCF_000092045.1:WP_011427116.1   9 KVVLAYSGGLDTSIILKWLQTElGAEVVTFTADLGQG-EELEPARKKAEMLGIKEIYIEDVREEFVRDF 76 
                                               8***********************************9.9****************************** PP

                                 TIGR00032  69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137
                                               +f+  +anavyeg+Yll+t++aRpli+k l+++a+k ga+a+ahG+tgKGnDqvRFels ++lnpd+k+
  lcl|NCBI__GCF_000092045.1:WP_011427116.1  77 VFPMFRANAVYEGVYLLGTSIARPLISKHLIDIARKTGADAIAHGATGKGNDQVRFELSAYALNPDIKI 145
                                               ********************************************************************* PP

                                 TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkd 203
                                               iaP+r++ +  R+e++++a+++ i+v+ +k  e ++s+D nll+ s E++ LEdp  e pe +++ + +
  lcl|NCBI__GCF_000092045.1:WP_011427116.1 146 IAPWRDWAFKsRTELLAFAEQHQIPVAKDKkgEAPFSVDANLLHSSSEGKVLEDPAQEAPEYVHMRTIS 214
                                               *********88***************988744689*********************************8 PP

                                 TIGR00032 204 piektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEap 272
                                               p++++ d++ v++++F+kG  v++ng++++p +l+ ++n  ++ +G+Gr+D vE+R +g+KsR++YE+p
  lcl|NCBI__GCF_000092045.1:WP_011427116.1 215 PEAAP-DKATVIKVGFRKGDAVSINGVEMSPATLLATLNTYGRDNGIGRLDLVENRFVGMKSRGVYETP 282
                                               88877.*************************************************************** PP

                                 TIGR00032 273 alllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklf 341
                                               + ++L++Ah+++e+ +l++  +++k+ +  +y+eliY+G+wf+p++e+l+ali+k+qe v G+v++kl+
  lcl|NCBI__GCF_000092045.1:WP_011427116.1 283 GGTILLSAHRAIESITLDRGAAHLKDEIMPRYAELIYYGFWFSPEREMLQALIDKSQEYVEGEVTLKLY 351
                                               ********************************************************************* PP

                                 TIGR00032 342 kGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvy 389
                                               kGn++vigr+se+slY+++lv+fe  + ++dqkda+Gfik+++l+ ++ 
  lcl|NCBI__GCF_000092045.1:WP_011427116.1 352 KGNVMVIGRESEKSLYSDKLVTFEDdQGAYDQKDAAGFIKLNALRLRTL 400
                                               ************************955689**************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (407 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: 00:00:00.01
# Mc/sec: 9.82
//
[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