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.5109.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[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:

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:

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:

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:

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