Alignments for a candidate for carA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Paraburkholderia bryophila 376MFSha3.1

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate H281DRAFT_04402 H281DRAFT_04402 carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Burk376:H281DRAFT_04402
          Length = 384

 Score =  496 bits (1276), Expect = e-145
 Identities = 243/371 (65%), Positives = 289/371 (77%), Gaps = 4/371 (1%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           ALL L DGT F G +IGA G  +GEVVFNT++TGYQEILTDPSY+RQIVTLTYPHIGNVG
Sbjct: 8   ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVG 67

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            N  D E+++VHA GL+IRDLP++ASNFR    L+ YL+   +VAIA +DTRKLTR+LR+
Sbjct: 68  VNAEDVEATKVHAAGLIIRDLPVLASNFRMERTLTQYLQDEGVVAIAGLDTRKLTRVLRD 127

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGAQNG I+AG + D A A+E AR+FPGL GMDLAK V+T E Y WTQ  W L  G    
Sbjct: 128 KGAQNGAILAGSD-DEAKAIELARSFPGLAGMDLAKVVSTKETYEWTQTEWRLESGYG-- 184

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
            K++   + VVA+D+G K NILRML +RGC +T++PA+ SA D L +NPDGIFLSNGPGD
Sbjct: 185 -KQNAPKYRVVAFDYGVKYNILRMLAERGCHVTVLPAEASAADALALNPDGIFLSNGPGD 243

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           P PCDYAI A ++ +E  IP FGICLGHQ++ LA GA+TVKMK GHHG NHPVKD++   
Sbjct: 244 PEPCDYAIAATKELIERGIPTFGICLGHQIMGLALGARTVKMKTGHHGANHPVKDLDDGR 303

Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364
           V+IT+QNHGFAVD  TLPAN RVTH SLFDGTLQG   +DKPAF FQGHPEASPGPHD A
Sbjct: 304 VIITSQNHGFAVDADTLPANARVTHVSLFDGTLQGFALSDKPAFCFQGHPEASPGPHDIA 363

Query: 365 PLFDHFIELIE 375
            LFD F  L++
Sbjct: 364 YLFDRFTALMD 374


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: 518
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: 382
Length of database: 384
Length adjustment: 30
Effective length of query: 352
Effective length of database: 354
Effective search space:   124608
Effective search space used:   124608
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 H281DRAFT_04402 H281DRAFT_04402 (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.7322.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.5e-147  477.2   0.0   1.7e-147  477.0   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04402  H281DRAFT_04402 carbamoyl-phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04402  H281DRAFT_04402 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.0   0.0  1.7e-147  1.7e-147       1     360 [.       8     374 ..       8     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 477.0 bits;  conditional E-value: 1.7e-147
                                    TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneeda 66 
                                                  a l+l+dGtvf+g+s+ga+++++GevvFnT++tGYqEiltDpsY++qiv+ltyp+ign+gvn+ed+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04402   8 ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVGVNAEDV 73 
                                                  579*************************************************************** PP

                                    TIGR01368  67 eskkikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistek 132
                                                  e++k++++gl++++l   +sn+r++++L+++l++eg+vai+g+DTR+l++ lR+kg+++++i + +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04402  74 EATKVHAAGLIIRDLPVLASNFRMERTLTQYLQDEGVVAIAGLDTRKLTRVLRDKGAQNGAILAGS 139
                                                  ****************************************************************** PP

                                    TIGR01368 133 sekeelvekakespkvkevnlvkevstkeayeleq.....k...akkegkklrvvvidlGvKenil 190
                                                   ++ +++e a++ p +++++l+k vstke+ye++q     +    k++  k+rvv++d+GvK nil
  lcl|FitnessBrowser__Burk376:H281DRAFT_04402 140 DDEAKAIELARSFPGLAGMDLAKVVSTKETYEWTQtewrlEsgyGKQNAPKYRVVAFDYGVKYNIL 205
                                                  **********************************976655166677888889************** PP

                                    TIGR01368 191 reLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGh 256
                                                  r+L++rg++vtv+pa++sa++  +lnpdgi+lsnGPGdP+ +++ai+ +k+l+e+ iP+fGIclGh
  lcl|FitnessBrowser__Burk376:H281DRAFT_04402 206 RMLAERGCHVTVLPAEASAADALALNPDGIFLSNGPGDPEPCDYAIAATKELIERGIPTFGICLGH 271
                                                  ****************************************************************** PP

                                    TIGR01368 257 qllalalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtv 322
                                                  q+++lalga+t+k+k Gh+GaNhpvkdl++grv itsqNHg+avd ++l+++ ++vthv+l+Dgt+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04402 272 QIMGLALGARTVKMKTGHHGANHPVKDLDDGRVIITSQNHGFAVDADTLPAN-ARVTHVSLFDGTL 336
                                                  ************************************************8866.9************ PP

                                    TIGR01368 323 eglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                                  +g + +++p+f  Q HPeaspGphd +ylFd+f+ l++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04402 337 QGFALSDKPAFCFQGHPEASPGPHDIAYLFDRFTALMD 374
                                                  **********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (384 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.31
//
[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