GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Salinicoccus carnicancri Crm

Align Carbamoyl-phosphate synthase pyrimidine-specific small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_017548471.1 C792_RS0105600 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P25993
         (364 letters)



>NCBI__GCF_000330705.1:WP_017548471.1
          Length = 363

 Score =  397 bits (1020), Expect = e-115
 Identities = 190/360 (52%), Positives = 256/360 (71%), Gaps = 3/360 (0%)

Query: 2   KRRLVLENGAVFEGEAFGSLEHNMGEVVFNTGMTGYQEILSDPSYCGQIVTLTYPLIGNY 61
           KR LVLE+G V+EG  FGS     GE+VFNT MTG QEI++D SY  QI+T +YPLIGN 
Sbjct: 5   KRYLVLEDGTVYEGYRFGSDRTAEGELVFNTAMTGAQEIITDLSYTDQIITFSYPLIGNT 64

Query: 62  GINRDDFESITPFVKGLIIKELCELPSNWRSAYTLDEYLKMKNIPGLQGIDTRKLTRMIR 121
           G+N +D E++ P  +G++++E C  PSN+R++ +LD +L+  NIPG+ G+DTR +TR IR
Sbjct: 65  GVNIEDNETLVPSARGVVVREACSEPSNFRASESLDSFLRRHNIPGISGVDTRSITRKIR 124

Query: 122 TAGALKGTFASSDEDIEAVLKRLNETELPRNQVSQVSAKTAYPSPGRGKRIVLVDFGMKH 181
             G +K    + DE+ E ++  L       +QV +VS +  Y S G GKR+VLVD+G K 
Sbjct: 125 DKGVMKAVM-TDDENHEELVGLLQNASFRTDQVKRVSTRAPYISTGPGKRVVLVDYGKKE 183

Query: 182 GILRELNKRKCDVIVVPYNITAEEVLQLKPDGIMLSNGPGDPKDVPEAIEMIKGVLGKVP 241
            I+R LN   CDV VVP++ TAE++L++KPDG+MLSNGPGDP+DV   I  +K ++G+VP
Sbjct: 184 NIVRSLNTHGCDVTVVPHDTTAEDILKMKPDGVMLSNGPGDPEDVEAGIRTVKNLIGRVP 243

Query: 242 LFGICLGHQLFALACGANTEKMKFGHRGSNHPVKELATGKVALTSQNHGYTV--SSISKT 299
           LFGICLGHQL  LACGA T KMKFGHRGSN PV   ATG+V +T+QNHG+ +   S+  T
Sbjct: 244 LFGICLGHQLIGLACGAKTFKMKFGHRGSNQPVINHATGRVEITAQNHGFAIDADSLGST 303

Query: 300 ELEVTHIAINDDTIEGLKHKTLPAFTVQYHPEASPGPEDANHLFDRFIEMIETTEKEGEA 359
            LE+TH A+ND T+EG++H   P F+VQYHPEAS GP D+ +LF  F+ M+ET ++   A
Sbjct: 304 GLEITHTALNDRTVEGVRHVKHPVFSVQYHPEASAGPHDSEYLFGEFVNMMETKKEANNA 363


Lambda     K      H
   0.317    0.136    0.397 

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: 399
Number of extensions: 16
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: 364
Length of database: 363
Length adjustment: 29
Effective length of query: 335
Effective length of database: 334
Effective search space:   111890
Effective search space used:   111890
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_017548471.1 C792_RS0105600 (glutamine-hydrolyzing 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.3412593.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.1e-150  485.3   0.1   5.9e-150  485.1   0.1    1.0  1  NCBI__GCF_000330705.1:WP_017548471.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017548471.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.1   0.1  5.9e-150  5.9e-150       2     360 ..       7     355 ..       6     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 485.1 bits;  conditional E-value: 5.9e-150
                             TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskkikvk 74 
                                           +lvledGtv+eg+ fg+++++ Ge+vFnT+mtG qEi+tD sY++qi++++yplign+gvn ed+e   + ++
  NCBI__GCF_000330705.1:WP_017548471.1   7 YLVLEDGTVYEGYRFGSDRTAEGELVFNTAMTGAQEIITDLSYTDQIITFSYPLIGNTGVNIEDNETLVPSAR 79 
                                           8************************************************************************ PP

                             TIGR01368  75 glvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeelvekakespk 147
                                           g+vv+e+++e+sn+ra+esL++fl++++i++i gvDTR++++k+R+kg+mkav+++++ ++eelv  ++++  
  NCBI__GCF_000330705.1:WP_017548471.1  80 GVVVREACSEPSNFRASESLDSFLRRHNIPGISGVDTRSITRKIRDKGVMKAVMTDDE-NHEELVGLLQNASF 151
                                           *****************************************************99998.66677775555544 PP

                             TIGR01368 148 vkevnlvkevstkeayeleqkakkegkklrvvvidlGvKenilreLvkrgvevtvvpadtsaeeikklnpdgi 220
                                              ++ vk+vst+ +y  +      g  +rvv++d+G Keni+r+L ++g++vtvvp+dt+ae+i k++pdg+
  NCBI__GCF_000330705.1:WP_017548471.1 152 R--TDQVKRVSTRAPYISTG----PG--KRVVLVDYGKKENIVRSLNTHGCDVTVVPHDTTAEDILKMKPDGV 216
                                           4..699**********7773....44..46******************************************* PP

                             TIGR01368 221 llsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgaktyklkfGhrGaNhpvkdlktgrveits 293
                                           +lsnGPGdP++ve+ i+tvk+l++ ++P+fGIclGhql++la gakt+k+kfGhrG+N+pv++++tgrveit+
  NCBI__GCF_000330705.1:WP_017548471.1 217 MLSNGPGDPEDVEAGIRTVKNLIG-RVPLFGICLGHQLIGLACGAKTFKMKFGHRGSNQPVINHATGRVEITA 288
                                           ************************.************************************************ PP

                             TIGR01368 294 qNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQyHPeaspGphdteylFdefvelik 360
                                           qNHg+a+d +sl ++ le+th+ lnD tveg++h + pvfsvQyHPeas+Gphd+eylF efv++++
  NCBI__GCF_000330705.1:WP_017548471.1 289 QNHGFAIDADSLGSTGLEITHTALNDRTVEGVRHVKHPVFSVQYHPEASAGPHDSEYLFGEFVNMME 355
                                           ****************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (363 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.65
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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