Alignments for a candidate for carA in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Desulfarculus baarsii DSM 2075

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate WP_013259916.1 DEBA_RS15625 carbamoyl-phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>NCBI__GCF_000143965.1:WP_013259916.1
          Length = 394

 Score =  353 bits (905), Expect = e-102
 Identities = 181/383 (47%), Positives = 250/383 (65%), Gaps = 10/383 (2%)

Query: 55  SYNARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIG 114
           S  A L LEDG+I+  ++F   G   AE+ FNT++TGYQE+LTDPSY GQ V+MT P IG
Sbjct: 2   SQKALLALEDGTIFWCRAFAGGGEVAAEVCFNTAMTGYQEVLTDPSYHGQMVVMTYPLIG 61

Query: 115 NTGVNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRR 174
           N GVNP+D ES    ++  +++      SN+R T +L  YL    +MGV  LDTRA+TR 
Sbjct: 62  NYGVNPEDVESAAVQVSAFLVKEYIDFPSNFRATASLRQYLEAAGVMGVEGLDTRALTRH 121

Query: 175 LREDGSLIGVLSTEQSKTDDELLQMSRSWDIVGIDLISDVSCKSPYEWVD-------KTN 227
           LR  G++ GVLST     +  + +   S  +VG+DL+ +V+C+  Y W D          
Sbjct: 122 LRMRGAMKGVLSTLDLDPESLVAKAKASPGLVGLDLVKNVTCQKAYRWQDGKPGPTLDLE 181

Query: 228 AEWDFNTNSRDGKS-YKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGI 286
            E+D       G+  ++V A D GIK NILRRL   GC + V+P+  PA   ++++PDG+
Sbjct: 182 GEFDAQAVWAGGQGRFRVAALDCGIKYNILRRLEKRGCNLVVLPAHTPAETIMRLDPDGV 241

Query: 287 LFSNGPGDPSAVPYAVETVKELLGKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPV 346
             SNGPGDPSAV Y VETV+ LLG+ P++GIC+GHQ++GQALGG+TFK+KFGH G N PV
Sbjct: 242 FLSNGPGDPSAVTYVVETVRRLLGQAPIFGICLGHQMIGQALGGRTFKLKFGHRGANQPV 301

Query: 347 RNNRTGQVEISAQNHNYAVDPASL-PGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEA 405
            +  T +VEI++QNH + VD  S+    + +TH+NLND +  GL+  ++ +  +QYHPEA
Sbjct: 302 MDLATAKVEITSQNHGFCVDDQSIDKTDILMTHMNLNDRTLEGLAHKKLPLFCVQYHPEA 361

Query: 406 SPGPHDSDNAFREFIELMKRSKQ 428
           SPGPHD+D  F  F E+M R+KQ
Sbjct: 362 SPGPHDADYLFDRFEEMM-RTKQ 383


Lambda     K      H
   0.316    0.134    0.403 

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: 478
Number of extensions: 18
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: 430
Length of database: 394
Length adjustment: 31
Effective length of query: 399
Effective length of database: 363
Effective search space:   144837
Effective search space used:   144837
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: 50 (23.9 bits)

Align candidate WP_013259916.1 DEBA_RS15625 (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.13539.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-153  495.9   0.0   3.6e-153  495.7   0.0    1.0  1  lcl|NCBI__GCF_000143965.1:WP_013259916.1  DEBA_RS15625 carbamoyl-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013259916.1  DEBA_RS15625 carbamoyl-phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.7   0.0  3.6e-153  3.6e-153       1     360 [.       5     380 ..       5     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 495.7 bits;  conditional E-value: 3.6e-153
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a l+ledGt+f  ++f+  +ev++ev+FnT+mtGYqE+ltDpsY+gq+vv+typlignygvn+ed+es 
  lcl|NCBI__GCF_000143965.1:WP_013259916.1   5 ALLALEDGTIFWCRAFAGGGEVAAEVCFNTAMTGYQEVLTDPSYHGQMVVMTYPLIGNYGVNPEDVESA 73 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138
                                                ++v++++vke+ + +sn+ra+ sL+++l+  g++++eg+DTRal+++lR +g+mk+v+st + + e+l
  lcl|NCBI__GCF_000143965.1:WP_013259916.1  74 AVQVSAFLVKEYIDFPSNFRATASLRQYLEAAGVMGVEGLDTRALTRHLRMRGAMKGVLSTLDLDPESL 142
                                               ********************************************************************* PP

                                 TIGR01368 139 vekakespkvkevnlvkevstkeayeleq...............k..akkegkklrvvvidlGvKenil 190
                                               v+kak+sp + +++lvk+v++++ay++++               +      + + rv+++d+G+K nil
  lcl|NCBI__GCF_000143965.1:WP_013259916.1 143 VAKAKASPGLVGLDLVKNVTCQKAYRWQDgkpgptldlegefdaQavWAGGQGRFRVAALDCGIKYNIL 211
                                               ****************************998888887766555425333444449************** PP

                                 TIGR01368 191 reLvkrgvevtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqll 259
                                               r+L krg++++v+pa+t+ae+i++l+pdg++lsnGPGdP+av++++etv++ll+ + PifGIclGhq++
  lcl|NCBI__GCF_000143965.1:WP_013259916.1 212 RRLEKRGCNLVVLPAHTPAETIMRLDPDGVFLSNGPGDPSAVTYVVETVRRLLG-QAPIFGICLGHQMI 279
                                               ******************************************************.************** PP

                                 TIGR01368 260 alalgaktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehk 328
                                               ++alg++t+klkfGhrGaN+pv+dl+t +veitsqNHg+ vd++s++++++ +th+nlnD t+egl+hk
  lcl|NCBI__GCF_000143965.1:WP_013259916.1 280 GQALGGRTFKLKFGHRGANQPVMDLATAKVEITSQNHGFCVDDQSIDKTDILMTHMNLNDRTLEGLAHK 348
                                               ********************************************************************* PP

                                 TIGR01368 329 elpvfsvQyHPeaspGphdteylFdefvelik 360
                                               +lp+f vQyHPeaspGphd++ylFd+f e+++
  lcl|NCBI__GCF_000143965.1:WP_013259916.1 349 KLPLFCVQYHPEASPGPHDADYLFDRFEEMMR 380
                                               ***************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (394 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: 00:00:00.02
# Mc/sec: 6.89
//
[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