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 SMa0693 SMa0693 arginine deiminase

Query= BRENDA::P13981
         (418 letters)



>FitnessBrowser__Smeli:SMa0693
          Length = 409

 Score =  532 bits (1370), Expect = e-156
 Identities = 249/410 (60%), Positives = 322/410 (78%), Gaps = 4/410 (0%)

Query: 8   LGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGI 67
           +GVHSE GKLR VMVC P LAHQRLTP NC +LLFDDVIWV++A++DH+DFV KM ERG+
Sbjct: 4   VGVHSEVGKLRTVMVCRPSLAHQRLTPGNCHDLLFDDVIWVHEAQKDHYDFVLKMEERGV 63

Query: 68  DVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGV 127
           +VLE+H+LL++T+ + EA K++LDR++  + +G  +   +R W+E ++ R+LA +LIGG+
Sbjct: 64  EVLELHDLLSDTLIDAEARKFVLDRRVAPNVMGSQIAELMRPWMEEMDSRRLAAFLIGGI 123

Query: 128 AADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQ 187
           +  DLP  +G  ++         + F+LPP+PNT F RD +CWIY GVT NPM+WPARR 
Sbjct: 124 SIADLPEGQGKALMA---SAFHSTQFVLPPIPNTLFQRDPSCWIYNGVTCNPMFWPARRA 180

Query: 188 ETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQ 247
           ETL+  A+YKFHP F  A F+IW+GD D+   ++T+EGGDVMPIG+G++L+GMGER++ Q
Sbjct: 181 ETLIQRAVYKFHPSFKGAAFDIWWGDSDEQFANATMEGGDVMPIGDGILLVGMGERTTYQ 240

Query: 248 AIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLR 307
           A+GQVA++LF  GAA RVI   +PKSRAAMHLDTVF+FCDRD+VT+F +VV +I  +SL 
Sbjct: 241 AVGQVAKALFKAGAATRVIGCLMPKSRAAMHLDTVFTFCDRDVVTLFADVVDQIRCYSLF 300

Query: 308 PDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPG 367
           P         +R+E++  LEVVAE+LG+ KLR + TGGN++ AEREQWDDGNNVV LEPG
Sbjct: 301 P-LDDEGNFEVRQEDRPMLEVVAEALGVDKLRTIATGGNTYEAEREQWDDGNNVVALEPG 359

Query: 368 VVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPID 417
           VVV YDRNTYTNTLLRKAG+EVITI  SELGRGRGGGHCMTCPI R+P D
Sbjct: 360 VVVAYDRNTYTNTLLRKAGIEVITIRGSELGRGRGGGHCMTCPIWREPTD 409


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: 538
Number of extensions: 13
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: 409
Length adjustment: 31
Effective length of query: 387
Effective length of database: 378
Effective search space:   146286
Effective search space used:   146286
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 SMa0693 SMa0693 (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.17023.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.6e-154  498.1   0.0   9.8e-154  497.9   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMa0693  SMa0693 arginine deiminase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa0693  SMa0693 arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.9   0.0  9.8e-154  9.8e-154       3     407 ..       6     407 ..       4     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 497.9 bits;  conditional E-value: 9.8e-154
                          TIGR01078   3 vysEiGkLkkvllhrPgkelenltPsnldelLFddilavedakkeHdeFveklrdngvevllledLlaEtlaasea 78 
                                        v+sE+GkL++v+++rP  ++++ltP n+++lLFdd+++v++a+k+H +Fv k+ ++gvevl+l+dLl++tl  +ea
  lcl|FitnessBrowser__Smeli:SMa0693   6 VHSEVGKLRTVMVCRPSLAHQRLTPGNCHDLLFDDVIWVHEAQKDHYDFVLKMEERGVEVLELHDLLSDTLIDAEA 81 
                                        9*************************************************************************** PP

                          TIGR01078  79 keklldealeeaeilgeelkkelreylksletrelvekllaGvakeelpeeedselslvdlevegdsefvidPlPn 154
                                        ++ +ld+ +   +++g+++++ +r +++++++r+l+  l++G+   +lpe + + l  +    + +++fv++P+Pn
  lcl|FitnessBrowser__Smeli:SMa0693  82 RKFVLDRRVA-PNVMGSQIAELMRPWMEEMDSRRLAAFLIGGISIADLPEGQGKAL--MASAFH-STQFVLPPIPN 153
                                        ********96.567***********************************9887665..555444.599******** PP

                          TIGR01078 155 llFtRDpsasigngvtlnkmalkaRqrEtlftelifkhHpkfanaevevyyd....rsekaslEGGDvlvlskdvl 226
                                        +lF RDps++i+ngvt n+m+++aR+ Etl +++++k+Hp f++a + ++++    +  +a++EGGDv+ +++++l
  lcl|FitnessBrowser__Smeli:SMa0693 154 TLFQRDPSCWIYNGVTCNPMFWPARRAETLIQRAVYKFHPSFKGAAFDIWWGdsdeQFANATMEGGDVMPIGDGIL 229
                                        ***************************************************9666566789*************** PP

                          TIGR01078 227 viGiseRtsaqsveklakslfkneaefkkvlaiklpkkralmHLDtvltmvDkdkftvfpevekelkafsiysltk 302
                                        ++G++eRt+ q+v+++ak+lfk  +++ +v+   +pk+ra+mHLDtv+t++D+d++t+f++v+++++ +s+  l +
  lcl|FitnessBrowser__Smeli:SMa0693 230 LVGMGERTTYQAVGQVAKALFKA-GAATRVIGCLMPKSRAAMHLDTVFTFCDRDVVTLFADVVDQIRCYSLFPLDD 304
                                        ***********************.*****************************************99999888887 PP

                          TIGR01078 303 gneekikveekakleevlaealgvkklkliktgGgdsveaeREqwnDgnnvlaiaPGvvvaYeRnvvtnallekaG 378
                                        +++ + + +e+ ++ ev+aealgv+kl+ i tg g+++eaeREqw+Dgnnv+a++PGvvvaY+Rn++tn+ll+kaG
  lcl|FitnessBrowser__Smeli:SMa0693 305 EGNFEVR-QEDRPMLEVVAEALGVDKLRTIATG-GNTYEAEREQWDDGNNVVALEPGVVVAYDRNTYTNTLLRKAG 378
                                        7554444.4889999*****************9.9***************************************** PP

                          TIGR01078 379 ikvltiagseLsrGrGgprCmsmplvRdd 407
                                        i+v+ti gseL+rGrGg++Cm++p+ R++
  lcl|FitnessBrowser__Smeli:SMa0693 379 IEVITIRGSELGRGRGGGHCMTCPIWREP 407
                                        ***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (408 nodes)
Target sequences:                          1  (409 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: 9.68
//
[ok]

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

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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