Alignments for a candidate for argH in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Sinorhizobium meliloti 1021

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate SM_b21094 SM_b21094 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>FitnessBrowser__Smeli:SM_b21094
          Length = 488

 Score =  467 bits (1201), Expect = e-136
 Identities = 241/452 (53%), Positives = 315/452 (69%), Gaps = 1/452 (0%)

Query: 3   TNEGSLWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRDG 62
           T    LWGGRF  GPS+ALA LS++    + L   D+  SRAH   L RAG+L E +   
Sbjct: 2   TEPTQLWGGRFKSGPSEALANLSRAPRSYFRLYKEDIAGSRAHASELKRAGVLDESEFSA 61

Query: 63  LLAGLDSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAALF 122
           + A L+ +  DV  G   P+  DED+H  LER L+ R+G  LGG+LRAGRSRNDQ A   
Sbjct: 62  IRAALEGIEADVGAGREEPIAADEDLHTFLERLLMARLGT-LGGKLRAGRSRNDQTANNT 120

Query: 123 RMWLRDAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHPLL 182
           R++LR   R ++ GV+ +  AL EQA+ H   +MPG THLQ AQP++L HHL+AHA  LL
Sbjct: 121 RLYLRRMARELSQGVIAIEEALTEQASRHTETVMPGFTHLQPAQPVVLGHHLMAHAQSLL 180

Query: 183 RDLDRIVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFSAAADNSVDATAARDFAAE 242
           RDL R  D+D+R   SP G+ ALAGS +   PD  A DLG+SAA +NS+DA AARD  AE
Sbjct: 181 RDLQRFADWDRRFDRSPLGAAALAGSGIARRPDLSAIDLGYSAACENSIDAVAARDHVAE 240

Query: 243 AAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGKSG 302
             F+ +++AVDLSRLAE+I +WSS +F +V LHDS+STGSSIMPQKKNPD+AEL RG SG
Sbjct: 241 FLFICSLVAVDLSRLAEEICLWSSKQFSWVRLHDSYSTGSSIMPQKKNPDVAELTRGMSG 300

Query: 303 RLIGNLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQRMA 362
            LIGN+AG LAT+KA PLAYNRDL EDK  +F+++  LEL+LPA AG+V +L F+V+++ 
Sbjct: 301 TLIGNIAGFLATMKAMPLAYNRDLAEDKRSLFETIDVLELVLPAFAGMVGTLEFDVEKLR 360

Query: 363 ELAPAGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISPEL 422
           E AP G+TLAT++A+WLV + VPF  AHE  GA VR  E+RG  L  LT ++L  I P L
Sbjct: 361 EEAPKGFTLATEVADWLVGRDVPFAEAHEITGAVVRFCEERGHDLAGLTAEDLPGIDPRL 420

Query: 423 TPQVREVLTIEGSVSARDCRGGTAPGRVAEQL 454
            P++   L +E ++++R+  G TAP +V EQ+
Sbjct: 421 HPEMLAALVLEKALASRNGYGATAPEKVREQI 452


Lambda     K      H
   0.318    0.133    0.382 

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: 571
Number of extensions: 21
Number of successful extensions: 2
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: 470
Length of database: 488
Length adjustment: 34
Effective length of query: 436
Effective length of database: 454
Effective search space:   197944
Effective search space used:   197944
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 SM_b21094 SM_b21094 (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.31764.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.7e-156  507.7   0.0     2e-156  507.5   0.0    1.1  1  lcl|FitnessBrowser__Smeli:SM_b21094  SM_b21094 argininosuccinate lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21094  SM_b21094 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.5   0.0    2e-156    2e-156       1     453 [.       7     458 ..       7     460 .. 0.99

  Alignments for each domain:
  == domain 1  score: 507.5 bits;  conditional E-value: 2e-156
                            TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklel 74 
                                          lwggR+k+++++a+a+++++ +   +l+++Di gs ah+  L++ag+l e e + +++aLe ++ +v +g+ e+
  lcl|FitnessBrowser__Smeli:SM_b21094   7 LWGGRFKSGPSEALANLSRAPRSYFRLYKEDIAGSRAHASELKRAGVLDESEFSAIRAALEGIEADVGAGREEP 80 
                                          7************************************************************************* PP

                            TIGR00838  75 evdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetl 148
                                             +eD+H+ +Er l++++g  +g+kl++grsRnDq a + rlylr   +el++ + ++ +al e+A +++et+
  lcl|FitnessBrowser__Smeli:SM_b21094  81 IAADEDLHTFLERLLMARLG-TLGGKLRAGRSRNDQTANNTRLYLRRMARELSQGVIAIEEALTEQASRHTETV 153
                                          ********************.***************************************************** PP

                            TIGR00838 149 mpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavven 222
                                          mpg+tHLq AqP+ l+Hhl+a+a++l rDl+R+ d  +R ++sPlG++Alag++ +  ++l+a +Lg++a++en
  lcl|FitnessBrowser__Smeli:SM_b21094 154 MPGFTHLQPAQPVVLGHHLMAHAQSLLRDLQRFADWDRRFDRSPLGAAALAGSGIARRPDLSAIDLGYSAACEN 227
                                          ************************************************************************** PP

                            TIGR00838 223 sldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgr 296
                                          s+dav++RD+++E+l+ ++l++v+lsrlaEe+ l+ss+ f++v l+d++s+gssimPqKKnpDvaEl Rg +g+
  lcl|FitnessBrowser__Smeli:SM_b21094 228 SIDAVAARDHVAEFLFICSLVAVDLSRLAEEICLWSSKQFSWVRLHDSYSTGSSIMPQKKNPDVAELTRGMSGT 301
                                          ************************************************************************** PP

                            TIGR00838 297 viGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAd 370
                                          +iGn++g+l+++Ka+PlaYn+Dl Edk +lf++++ +e +l +++g++ +l++  e+l+e a k+f+lat++Ad
  lcl|FitnessBrowser__Smeli:SM_b21094 302 LIGNIAGFLATMKAMPLAYNRDLAEDKRSLFETIDVLELVLPAFAGMVGTLEFDVEKLREEAPKGFTLATEVAD 375
                                          ************************************************************************** PP

                            TIGR00838 371 ylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeeve 444
                                          +lv + vPF eahei+G+vv+ ++e+G +l  lt e l  ++++l++++l +l le+a++ r+ +G ta+e+v+
  lcl|FitnessBrowser__Smeli:SM_b21094 376 WLVGRDVPFAEAHEITGAVVRFCEERGHDLAGLTAEDLPGIDPRLHPEMLAALVLEKALASRNGYGATAPEKVR 449
                                          ************************************************************************** PP

                            TIGR00838 445 kaieeakae 453
                                          ++i+ +++ 
  lcl|FitnessBrowser__Smeli:SM_b21094 450 EQIARFETA 458
                                          ***998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (488 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: 8.84
//
[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