Alignments for a candidate for carA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Cupriavidus basilensis 4G11

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate RR42_RS13520 RR42_RS13520 carbamoyl phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Cup4G11:RR42_RS13520
          Length = 378

 Score =  509 bits (1311), Expect = e-149
 Identities = 247/376 (65%), Positives = 296/376 (78%), Gaps = 4/376 (1%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           SA+L L DGT F G +IGA+G  +GEVVFNT++TGYQEILTDPSYSRQIVTLTYPHIGNV
Sbjct: 7   SAILALADGTVFRGYSIGASGHTIGEVVFNTALTGYQEILTDPSYSRQIVTLTYPHIGNV 66

Query: 64  GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123
           G N  D E+++VHA GL+I+DLPL+ASNFR    L  YLK+  +VAIA IDTRKLTR+LR
Sbjct: 67  GVNTEDVEATKVHAAGLIIKDLPLLASNFRKEHSLGHYLKQEKVVAIAGIDTRKLTRILR 126

Query: 124 EKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPE 183
           EKGAQNGCI+AG++ +   A++ AR+FPGL GMDLAK V+  E Y W Q  W L  G   
Sbjct: 127 EKGAQNGCILAGED-NVQKAIDLARSFPGLAGMDLAKVVSVKEPYEWNQTEWVLGQGYG- 184

Query: 184 AKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPG 243
             K +   FHVVA+D+G K NILRML  RGC++T++PAQ SAED L +NPDG+FLSNGPG
Sbjct: 185 --KLESPRFHVVAFDYGVKFNILRMLAARGCKVTVLPAQASAEDALALNPDGVFLSNGPG 242

Query: 244 DPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKN 303
           DP PCDYAI A ++F+   IP FGICLGHQ++ALA+GAKT+KMKFGHHG NHPVKD++  
Sbjct: 243 DPEPCDYAIRATREFIARGIPTFGICLGHQIMALAAGAKTLKMKFGHHGANHPVKDLDDG 302

Query: 304 VVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDA 363
            V+IT+QNHGFAVD  TLPAN+R TH SLFDG+LQG   TDKPAF FQGHPEASPGPHD 
Sbjct: 303 RVVITSQNHGFAVDADTLPANVRATHVSLFDGSLQGFALTDKPAFCFQGHPEASPGPHDV 362

Query: 364 APLFDHFIELIEQYRK 379
           A LFD F +++   R+
Sbjct: 363 AYLFDRFTKMMADARQ 378


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: 521
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: 382
Length of database: 378
Length adjustment: 30
Effective length of query: 352
Effective length of database: 348
Effective search space:   122496
Effective search space used:   122496
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 RR42_RS13520 RR42_RS13520 (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.22438.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-149  482.7   0.0   3.7e-149  482.5   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS13520  RR42_RS13520 carbamoyl phosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS13520  RR42_RS13520 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.5   0.0  3.7e-149  3.7e-149       1     360 [.       8     374 ..       8     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 482.5 bits;  conditional E-value: 3.7e-149
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a+l+l+dGtvf+g+s+ga+++++GevvFnT++tGYqEiltDpsY++qiv+ltyp+ign+gvn+ed+e++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13520   8 AILALADGTVFRGYSIGASGHTIGEVVFNTALTGYQEILTDPSYSRQIVTLTYPHIGNVGVNTEDVEAT 76 
                                               689****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138
                                               k++++gl++k+l   +sn+r+++sL ++lk+e++vai+g+DTR+l++ lRekg+++++i + + + +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13520  77 KVHAAGLIIKDLPLLASNFRKEHSLGHYLKQEKVVAIAGIDTRKLTRILREKGAQNGCILAGEDNVQKA 145
                                               ********************************************************************* PP

                                 TIGR01368 139 vekakespkvkevnlvkevstkeayeleq......k..akkegkklrvvvidlGvKenilreLvkrgve 199
                                               ++ a++ p +++++l+k vs+ke+ye++q      +   k e+ + +vv++d+GvK nilr+L++rg++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13520 146 IDLARSFPGLAGMDLAKVVSVKEPYEWNQtewvlgQgyGKLESPRFHVVAFDYGVKFNILRMLAARGCK 214
                                               ****************************966655526567788889*********************** PP

                                 TIGR01368 200 vtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgakty 268
                                               vtv+pa++sae+  +lnpdg++lsnGPGdP+ +++ai+ +++++ + iP+fGIclGhq++ala+gakt+
  lcl|FitnessBrowser__Cup4G11:RR42_RS13520 215 VTVLPAQASAEDALALNPDGVFLSNGPGDPEPCDYAIRATREFIARGIPTFGICLGHQIMALAAGAKTL 283
                                               ********************************************************************* PP

                                 TIGR01368 269 klkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQy 337
                                               k+kfGh+GaNhpvkdl++grv itsqNHg+avd ++l+++ +++thv+l+Dg+++g + +++p+f  Q 
  lcl|FitnessBrowser__Cup4G11:RR42_RS13520 284 KMKFGHHGANHPVKDLDDGRVVITSQNHGFAVDADTLPAN-VRATHVSLFDGSLQGFALTDKPAFCFQG 351
                                               ************************************8866.**************************** PP

                                 TIGR01368 338 HPeaspGphdteylFdefvelik 360
                                               HPeaspGphd +ylFd+f+++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13520 352 HPEASPGPHDVAYLFDRFTKMMA 374
                                               *******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (378 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: 10.84
//
[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