Alignments for a candidate for carA in Rhizobium leguminosarum WSM1325

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Rhizobium leguminosarum WSM1325

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_011652894.1 RLEG_RS14640 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000023185.1:WP_011652894.1
          Length = 401

 Score =  371 bits (952), Expect = e-107
 Identities = 198/382 (51%), Positives = 249/382 (65%), Gaps = 12/382 (3%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           +ALLVL DGT   G+ IGATG    EVVFNT++TGY+EILTDPSY  QIVT T+PHIGN+
Sbjct: 13  TALLVLADGTVIEGKGIGATGKVPAEVVFNTALTGYEEILTDPSYLGQIVTFTFPHIGNI 72

Query: 64  GTNDADEE----SSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119
           GTND D E    +++  A G++ +      SN+R  + L  +LK   ++ +  IDTR LT
Sbjct: 73  GTNDEDIEDLTPAARHGAVGVIFKADITEPSNYRAAKHLDQWLKARGVIGLCGIDTRALT 132

Query: 120 RLLREKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSW 175
             +RE GA N  +IA D P+    +E    +A+A+ GL G+DLAK  ++ ++  WT+  W
Sbjct: 133 AWIRENGAPNA-VIAHD-PNGVFDIETLKAEAKAWSGLEGLDLAKIASSGQSSQWTETPW 190

Query: 176 TLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDG 235
               G  E K  D   +HVV  D+G KRNILR+     C++T+VPA TSAEDVL M PDG
Sbjct: 191 VWNEGYGELKATDA-KYHVVCLDYGVKRNILRLFAGLDCKVTVVPAATSAEDVLAMQPDG 249

Query: 236 IFLSNGPGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGN 294
           IFLSNGPGDPA   DYA+  I+  ++TDIPVFGICLGHQ+L LA GAKT KM  GHHG N
Sbjct: 250 IFLSNGPGDPAATGDYAVPVIKTLIKTDIPVFGICLGHQMLGLALGAKTEKMHQGHHGAN 309

Query: 295 HPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHP 354
           HPVKD     V I + NHGFAVD  +LP  +  TH SLFDGT  G+    K  FS Q HP
Sbjct: 310 HPVKDHTTGKVEIVSMNHGFAVDSKSLPDGVEETHISLFDGTNCGLRVLGKQVFSVQHHP 369

Query: 355 EASPGPHDAAPLFDHFIELIEQ 376
           EASPGP D+  LF  FI ++ +
Sbjct: 370 EASPGPQDSHYLFRRFINMVRE 391


Lambda     K      H
   0.318    0.135    0.400 

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: 471
Number of extensions: 21
Number of successful extensions: 5
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: 382
Length of database: 401
Length adjustment: 31
Effective length of query: 351
Effective length of database: 370
Effective search space:   129870
Effective search space used:   129870
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: 50 (23.9 bits)

Align candidate WP_011652894.1 RLEG_RS14640 (carbamoyl-phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

# 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/TIGR01368.hmm
# target sequence database:        /tmp/gapView.12110.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01368  [M=361]
Accession:   TIGR01368
Description: CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-130  421.4   0.0   1.6e-130  421.2   0.0    1.0  1  lcl|NCBI__GCF_000023185.1:WP_011652894.1  RLEG_RS14640 carbamoyl-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_011652894.1  RLEG_RS14640 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  421.2   0.0  1.6e-130  1.6e-130       1     360 [.      14     390 ..      14     391 .. 0.94

  Alignments for each domain:
  == domain 1  score: 421.2 bits;  conditional E-value: 1.6e-130
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a lvl+dGtv+egk++ga+++v +evvFnT++tGY+EiltDpsY gqiv++t p+ign+g+n+ed+e  
  lcl|NCBI__GCF_000023185.1:WP_011652894.1  14 ALLVLADGTVIEGKGIGATGKVPAEVVFNTALTGYEEILTDPSYLGQIVTFTFPHIGNIGTNDEDIEDL 82 
                                               579***************************************************************866 PP

                                 TIGR01368  70 ....kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse 134
                                                   +  + g++ k   +e+snyra + L+++lk +g++++ g+DTRal+  +Re+g+ +avi+++ + 
  lcl|NCBI__GCF_000023185.1:WP_011652894.1  83 tpaaRHGAVGVIFKADITEPSNYRAAKHLDQWLKARGVIGLCGIDTRALTAWIRENGAPNAVIAHDPNG 151
                                               222255678*******************************************************99976 PP

                                 TIGR01368 135 ...keelvekakespkvkevnlvkevstkeayeleq..........kakkegkklrvvvidlGvKenil 190
                                                   e+l+++ak+   +++++l+k +s  + +++++          + k+++ k++vv +d+GvK+nil
  lcl|NCBI__GCF_000023185.1:WP_011652894.1 152 vfdIETLKAEAKAWSGLEGLDLAKIASSGQSSQWTEtpwvwnegygELKATDAKYHVVCLDYGVKRNIL 220
                                               666788999999999*******************997777765554488889999************** PP

                                 TIGR01368 191 reLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhql 258
                                               r ++  +++vtvvpa tsae++ +++pdgi+lsnGPGdPaa  ++a+  +k+l++++iP+fGIclGhq+
  lcl|NCBI__GCF_000023185.1:WP_011652894.1 221 RLFAGLDCKVTVVPAATSAEDVLAMQPDGIFLSNGPGDPAATgDYAVPVIKTLIKTDIPVFGICLGHQM 289
                                               ***************************************87626789999******************* PP

                                 TIGR01368 259 lalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtvegleh 327
                                               l+lalgakt k++ Gh+GaNhpvkd++tg+vei s NHg+avd++sl+ + +e th +l+Dgt+ gl+ 
  lcl|NCBI__GCF_000023185.1:WP_011652894.1 290 LGLALGAKTEKMHQGHHGANHPVKDHTTGKVEIVSMNHGFAVDSKSLPDG-VEETHISLFDGTNCGLRV 357
                                               **********************************************8855.****************** PP

                                 TIGR01368 328 kelpvfsvQyHPeaspGphdteylFdefvelik 360
                                                 ++vfsvQ+HPeaspGp+d++ylF++f+++++
  lcl|NCBI__GCF_000023185.1:WP_011652894.1 358 LGKQVFSVQHHPEASPGPQDSHYLFRRFINMVR 390
                                               ******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (401 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: 00:00:00.01
# Mc/sec: 11.02
//
[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