Alignments for a candidate for carA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Synechococcus elongatus PCC 7942

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate Synpcc7942_2122 Synpcc7942_2122 carbamoyl phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__SynE:Synpcc7942_2122
          Length = 391

 Score =  370 bits (950), Expect = e-107
 Identities = 182/368 (49%), Positives = 253/368 (68%), Gaps = 4/368 (1%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A LVL DGS++   + GA GT I E+VFNT +TGYQE+LTDPSY GQ V  T P++GNTG
Sbjct: 19  ALLVLADGSVFHGYACGAAGTVIGEVVFNTGMTGYQEVLTDPSYCGQIVSFTYPELGNTG 78

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           VNP+DEES +  ++GL+ RN++   SNWR  ++L DYL + +I+G+Y +DTRA+T+ LR 
Sbjct: 79  VNPEDEESARPQVSGLIARNVARRHSNWRADRSLPDYLQQHNIVGIYGIDTRALTQHLRS 138

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSWDIVGIDLISDVSCKSPYEWVDKTNAEWDFNTNSR 237
            G++ G +ST     ++   ++  +  + G++L+  V+   PYEW   T+  W+F     
Sbjct: 139 TGAMNGGISTTILDPEELWAEVKAAPSMEGLNLVDQVTTDRPYEWQTPTSQTWEF-IEGP 197

Query: 238 DGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGPGDPSA 297
             +S  V+A DFG+K+NILRRL+SYGC++ VVP+  P  E L+  PDG+  SNGPGDP+ 
Sbjct: 198 TTESLTVVAIDFGVKRNILRRLASYGCRVIVVPADTPIEEILRHEPDGVFLSNGPGDPAT 257

Query: 298 VPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRTGQVEI 356
           V   + T + LL   +P++GIC+GHQ+LG ALG +TFK+KFGH G NHP     + QVEI
Sbjct: 258 VKNGISTAQALLQTGLPLFGICLGHQILGLALGAQTFKLKFGHRGLNHPC--GLSQQVEI 315

Query: 357 SAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHDSDNAF 416
           ++QNH +A+   SL   VEVTH+NLND + AGL    + V S+QYHPEASPGPHDSD  F
Sbjct: 316 TSQNHGFAIAADSLGPDVEVTHLNLNDRTVAGLRHRHLPVFSVQYHPEASPGPHDSDYLF 375

Query: 417 REFIELMK 424
            +F+ LM+
Sbjct: 376 EQFVALMR 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: 496
Number of extensions: 26
Number of successful extensions: 4
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: 391
Length adjustment: 31
Effective length of query: 399
Effective length of database: 360
Effective search space:   143640
Effective search space used:   143640
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 Synpcc7942_2122 Synpcc7942_2122 (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.14505.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-157  510.6   0.0   1.2e-157  510.4   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2122  Synpcc7942_2122 carbamoyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2122  Synpcc7942_2122 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.4   0.0  1.2e-157  1.2e-157       1     360 [.      19     383 ..      19     384 .. 0.97

  Alignments for each domain:
  == domain 1  score: 510.4 bits;  conditional E-value: 1.2e-157
                                 TIGR01368   1 atlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaesk 69 
                                               a lvl+dG+vf+g++ ga ++v+GevvFnT+mtGYqE+ltDpsY gqiv +typ++gn+gvn+ed+es 
  lcl|FitnessBrowser__SynE:Synpcc7942_2122  19 ALLVLADGSVFHGYACGAAGTVIGEVVFNTGMTGYQEVLTDPSYCGQIVSFTYPELGNTGVNPEDEESA 87 
                                               579****************************************************************** PP

                                 TIGR01368  70 kikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavisteksekeel 138
                                               +++v+gl+ ++++++ sn+ra +sL ++l++++iv+i+g+DTRal+++lR++g+m++ ist+  + eel
  lcl|FitnessBrowser__SynE:Synpcc7942_2122  88 RPQVSGLIARNVARRHSNWRADRSLPDYLQQHNIVGIYGIDTRALTQHLRSTGAMNGGISTTILDPEEL 156
                                               ********************************************************************* PP

                                 TIGR01368 139 vekakespkvkevnlvkevstkeayeleq...k....akkegkk.lrvvvidlGvKenilreLvkrgve 199
                                                +++k++p+++++nlv++v+t+++ye+++   +    ++  +++ l+vv+id+GvK+nilr+L+++g++
  lcl|FitnessBrowser__SynE:Synpcc7942_2122 157 WAEVKAAPSMEGLNLVDQVTTDRPYEWQTptsQtwefIEGPTTEsLTVVAIDFGVKRNILRRLASYGCR 225
                                               ****************************977625556444444449*********************** PP

                                 TIGR01368 200 vtvvpadtsaeeikklnpdgillsnGPGdPaaveeaietvkklleakiPifGIclGhqllalalgakty 268
                                               v+vvpadt++eei + +pdg++lsnGPGdPa+v++ i+t ++ll++ +P+fGIclGhq+l+lalga+t+
  lcl|FitnessBrowser__SynE:Synpcc7942_2122 226 VIVVPADTPIEEILRHEPDGVFLSNGPGDPATVKNGISTAQALLQTGLPLFGICLGHQILGLALGAQTF 294
                                               ********************************************************************* PP

                                 TIGR01368 269 klkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfsvQy 337
                                               klkfGhrG Nhp+    +++veitsqNHg+a+  +sl   ++evth nlnD tv+gl+h++lpvfsvQy
  lcl|FitnessBrowser__SynE:Synpcc7942_2122 295 KLKFGHRGLNHPCG--LSQQVEITSQNHGFAIAADSLGP-DVEVTHLNLNDRTVAGLRHRHLPVFSVQY 360
                                               *************9..799*****************775.5**************************** PP

                                 TIGR01368 338 HPeaspGphdteylFdefvelik 360
                                               HPeaspGphd++ylF++fv l++
  lcl|FitnessBrowser__SynE:Synpcc7942_2122 361 HPEASPGPHDSDYLFEQFVALMR 383
                                               *******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (391 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: 9.82
//
[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