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.5008.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: 11.05
//
[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