Alignments for a candidate for arcA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcA in Sinorhizobium meliloti 1021

Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate SMa1670 SMa1670 arginine deiminase

Query= BRENDA::P13981
         (418 letters)



>FitnessBrowser__Smeli:SMa1670
          Length = 419

 Score =  570 bits (1469), Expect = e-167
 Identities = 268/417 (64%), Positives = 335/417 (80%), Gaps = 3/417 (0%)

Query: 2   STEKTKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTK 61
           ST+ T  GVHSE G+LRKVMVC+PG AHQRLTPSNCD LLFDDV+WV+ A+RDHFDF+TK
Sbjct: 6   STQHT-FGVHSEVGQLRKVMVCAPGRAHQRLTPSNCDALLFDDVLWVDNARRDHFDFMTK 64

Query: 62  MRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAE 121
           MR+RG++V+EMHNLL +T+  PEA KWILD ++  + VGL L  E+RS+LE L  R+LAE
Sbjct: 65  MRDRGVEVVEMHNLLAQTVAIPEARKWILDNQVVPNQVGLELLDEIRSYLEGLPDRELAE 124

Query: 122 YLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMY 181
            LIGG++  + P + G  +L++ R+  G + +LLPPLPNT +TRDTTCWIYGGVTLNP+Y
Sbjct: 125 TLIGGLSTHEFPETHGGEMLELIRDAAGVAEYLLPPLPNTLYTRDTTCWIYGGVTLNPLY 184

Query: 182 WPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMG 241
           WPAR +ET+L TAIYKFHP+F   +  +W+G+P  D G +TLEGGDVMPIG G VLIGM 
Sbjct: 185 WPARHEETILATAIYKFHPDFV-GKVNVWWGEPTTDWGLATLEGGDVMPIGKGNVLIGMS 243

Query: 242 ERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEI 301
           ER+SRQAI Q+A +LF KGAA+RVIVA +PK RAAMHLDTVF+F DRD V ++P++V EI
Sbjct: 244 ERTSRQAISQLAATLFEKGAAQRVIVAAMPKLRAAMHLDTVFTFADRDCVLIYPDIVNEI 303

Query: 302 VPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNV 361
             FS RP    P  + + ++  +F+E V ++LGLK++RVVETGGN++  ER QWD G N+
Sbjct: 304 EAFSYRPG-EKPGSLELHKDRGSFVETVRDALGLKEMRVVETGGNAYVRERTQWDSGANL 362

Query: 362 VCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPIDY 418
           VCL PGVV+ YDRNTYTNTLLRKAGVEVITI+ +ELGRGRGGGHCMTCPI+RD +DY
Sbjct: 363 VCLSPGVVLAYDRNTYTNTLLRKAGVEVITITGAELGRGRGGGHCMTCPIIRDAVDY 419


Lambda     K      H
   0.319    0.137    0.414 

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: 598
Number of extensions: 17
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: 418
Length of database: 419
Length adjustment: 32
Effective length of query: 386
Effective length of database: 387
Effective search space:   149382
Effective search space used:   149382
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 SMa1670 SMa1670 (arginine deiminase)
to HMM TIGR01078 (arcA: arginine deiminase (EC 3.5.3.6))

# 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/TIGR01078.hmm
# target sequence database:        /tmp/gapView.8383.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01078  [M=408]
Accession:   TIGR01078
Description: arcA: arginine deiminase
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-152  492.5   0.0   4.8e-152  492.3   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMa1670  SMa1670 arginine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa1670  SMa1670 arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.3   0.0  4.8e-152  4.8e-152       3     408 .]      13     417 ..      11     417 .. 0.97

  Alignments for each domain:
  == domain 1  score: 492.3 bits;  conditional E-value: 4.8e-152
                          TIGR01078   3 vysEiGkLkkvllhrPgkelenltPsnldelLFddilavedakkeHdeFveklrdngvevllledLlaEtlaasea 78 
                                        v+sE+G+L+kv+++ Pg+++++ltPsn+d lLFdd+l+v++a+++H +F +k+rd+gvev+++++Lla t+a++ea
  lcl|FitnessBrowser__Smeli:SMa1670  13 VHSEVGQLRKVMVCAPGRAHQRLTPSNCDALLFDDVLWVDNARRDHFDFMTKMRDRGVEVVEMHNLLAQTVAIPEA 88 
                                        9*************************************************************************** PP

                          TIGR01078  79 keklldealeeaeilgeelkkelreylksletrelvekllaGvakeelpeeedselslvdlevegdsefvidPlPn 154
                                        ++++ld+++  ++ +g el  e+r+yl+ l +rel+e+l++G+ ++e+pe++  e+    + + g  e++++PlPn
  lcl|FitnessBrowser__Smeli:SMa1670  89 RKWILDNQVVPNQ-VGLELLDEIRSYLEGLPDRELAETLIGGLSTHEFPETHGGEMLELIRDAAGVAEYLLPPLPN 163
                                        *************.9***************************************99999999************** PP

                          TIGR01078 155 llFtRDpsasigngvtlnkmalkaRqrEtlftelifkhHpkfanaevevyyd....rsekaslEGGDvlvlskdvl 226
                                        +l+tRD++++i++gvtln+++++aR+ Et+++++i+k+Hp f ++ v+v+++    ++  a+lEGGDv+ ++k+ +
  lcl|FitnessBrowser__Smeli:SMa1670 164 TLYTRDTTCWIYGGVTLNPLYWPARHEETILATAIYKFHPDFVGK-VNVWWGepttDWGLATLEGGDVMPIGKGNV 238
                                        ********************************************6.99999989889999**************** PP

                          TIGR01078 227 viGiseRtsaqsveklakslfkneaefkkvlaiklpkkralmHLDtvltmvDkdkftvfpevekelkafsiysltk 302
                                        +iG+seRts+q++ +la++lf++ +++++v+++ +pk ra+mHLDtv+t+ D+d ++++p++++e++afs +  +k
  lcl|FitnessBrowser__Smeli:SMa1670 239 LIGMSERTSRQAISQLAATLFEK-GAAQRVIVAAMPKLRAAMHLDTVFTFADRDCVLIYPDIVNEIEAFSYRPGEK 313
                                        **********************9.*********************************************9999887 PP

                          TIGR01078 303 gneekikveekakleevlaealgvkklkliktgGgdsveaeREqwnDgnnvlaiaPGvvvaYeRnvvtnallekaG 378
                                         ++  +  +++ ++ e +++alg+k++++++tg g++++ eR qw+ g+n +++ PGvv+aY+Rn++tn+ll+kaG
  lcl|FitnessBrowser__Smeli:SMa1670 314 PGS-LELHKDRGSFVETVRDALGLKEMRVVETG-GNAYVRERTQWDSGANLVCLSPGVVLAYDRNTYTNTLLRKAG 387
                                        754.5556699**********************.9***************************************** PP

                          TIGR01078 379 ikvltiagseLsrGrGgprCmsmplvRddi 408
                                        ++v+ti+g eL+rGrGg++Cm++p+ Rd +
  lcl|FitnessBrowser__Smeli:SMa1670 388 VEVITITGAELGRGRGGGHCMTCPIIRDAV 417
                                        ***************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (419 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.23
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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