Alignments for a candidate for carA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for carA in Azospirillum brasilense Sp245

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate AZOBR_RS10920 AZOBR_RS10920 carbamoyl phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__azobra:AZOBR_RS10920
          Length = 391

 Score =  406 bits (1043), Expect = e-118
 Identities = 206/377 (54%), Positives = 260/377 (68%), Gaps = 10/377 (2%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           + +LVL DGT F GR IGA G +VGEV FNTSMTGYQEILTDPSY+ QI+T T+PHIGN 
Sbjct: 15  TGVLVLADGTVFKGRGIGAVGDSVGEVCFNTSMTGYQEILTDPSYAGQIITFTFPHIGNT 74

Query: 64  GTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLR 123
           G N  D E+    A+GL++R      SN+R T  L  +LK + +V +A +DTR+LTR +R
Sbjct: 75  GANPEDIETVTPAARGLILRADVTDPSNWRATRHLDDWLKSYGLVGLAGVDTRRLTRRIR 134

Query: 124 EKGAQNGCIIAGDNPDAALALE----KARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTG 179
           + GA NG  +    PD    L+    KA+ +PGL GMDLAK+V+  + Y W +G+WTL  
Sbjct: 135 DLGAPNG--VVAHAPDGKFDLDALVAKAKGWPGLEGMDLAKDVSCRQTYGWDEGAWTLGA 192

Query: 180 GLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLS 239
           G      ++   FHVVA DFGAKRNILR L   GC++T+VP   + EDV++  PDG+FLS
Sbjct: 193 GYAT---QESPRFHVVAIDFGAKRNILRCLAAAGCKVTVVPGTATVEDVMRHKPDGVFLS 249

Query: 240 NGPGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVK 298
           NGPGDPA   +YA+  I+  L+T +P+FGICLGHQ+L+LA GAKT KM  GH G NHPVK
Sbjct: 250 NGPGDPAATGEYAVPTIKGLLDTGLPMFGICLGHQMLSLALGAKTKKMPLGHRGANHPVK 309

Query: 299 DVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358
           D+    V IT+QNHGF V E TLPA+  VTH SLFDGT +GI   +KP FS Q HPEASP
Sbjct: 310 DLASGRVEITSQNHGFVVMEETLPADAEVTHVSLFDGTNEGIRLKNKPVFSVQYHPEASP 369

Query: 359 GPHDAAPLFDHFIELIE 375
           GP D+  LFD F+ L++
Sbjct: 370 GPQDSHYLFDRFVALMD 386


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: 491
Number of extensions: 16
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: 382
Length of database: 391
Length adjustment: 30
Effective length of query: 352
Effective length of database: 361
Effective search space:   127072
Effective search space used:   127072
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 AZOBR_RS10920 AZOBR_RS10920 (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.10081.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-143  463.6   0.0   2.4e-143  463.4   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS10920  AZOBR_RS10920 carbamoyl phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS10920  AZOBR_RS10920 carbamoyl phosphate synthase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.4   0.0  2.4e-143  2.4e-143       2     360 ..      17     386 ..      16     387 .. 0.95

  Alignments for each domain:
  == domain 1  score: 463.4 bits;  conditional E-value: 2.4e-143
                                 TIGR01368   2 tlvledGtvfegksfgaekevvGevvFnTsmtGYqEiltDpsYkgqivvltyplignygvneedaeskk 70 
                                               +lvl+dGtvf+g+++ga ++ vGev+FnTsmtGYqEiltDpsY+gqi+++t p+ign+g n+ed+e  +
  lcl|FitnessBrowser__azobra:AZOBR_RS10920  17 VLVLADGTVFKGRGIGAVGDSVGEVCFNTSMTGYQEILTDPSYAGQIITFTFPHIGNTGANPEDIETVT 85 
                                               69******************************************************************* PP

                                 TIGR01368  71 ikvkglvvkelskevsnyrakesLeeflkeegivaiegvDTRalvkklRekgsmkavistekse...ke 136
                                               + ++gl+++   +++sn+ra++ L+++lk++g+v+++gvDTR l++++R+ g+ ++v++++       +
  lcl|FitnessBrowser__azobra:AZOBR_RS10920  86 PAARGLILRADVTDPSNWRATRHLDDWLKSYGLVGLAGVDTRRLTRRIRDLGAPNGVVAHAPDGkfdLD 154
                                               ***********************************************************9875544478 PP

                                 TIGR01368 137 elvekakespkvkevnlvkevstkeayeleq.....k...akkegkklrvvvidlGvKenilreLvkrg 197
                                                lv+kak  p +++++l+k+vs++++y + +         a++e+ + +vv+id+G K+nilr+L++ g
  lcl|FitnessBrowser__azobra:AZOBR_RS10920 155 ALVAKAKGWPGLEGMDLAKDVSCRQTYGWDEgawtlGagyATQESPRFHVVAIDFGAKRNILRCLAAAG 223
                                               9999999***********************97665515657788888********************** PP

                                 TIGR01368 198 vevtvvpadtsaeeikklnpdgillsnGPGdPaav.eeaietvkklleakiPifGIclGhqllalalga 265
                                               ++vtvvp ++++e++++ +pdg++lsnGPGdPaa  e+a+ t+k ll++ +P+fGIclGhq+l+lalga
  lcl|FitnessBrowser__azobra:AZOBR_RS10920 224 CKVTVVPGTATVEDVMRHKPDGVFLSNGPGDPAATgEYAVPTIKGLLDTGLPMFGICLGHQMLSLALGA 292
                                               ********************************77637889***************************** PP

                                 TIGR01368 266 ktyklkfGhrGaNhpvkdlktgrveitsqNHgyavdeeslkeeelevthvnlnDgtveglehkelpvfs 334
                                               kt k+  GhrGaNhpvkdl++grveitsqNHg++v ee+l+++ +evthv+l+Dgt+eg++ k++pvfs
  lcl|FitnessBrowser__azobra:AZOBR_RS10920 293 KTKKMPLGHRGANHPVKDLASGRVEITSQNHGFVVMEETLPAD-AEVTHVSLFDGTNEGIRLKNKPVFS 360
                                               ***************************************8855.************************* PP

                                 TIGR01368 335 vQyHPeaspGphdteylFdefvelik 360
                                               vQyHPeaspGp+d++ylFd+fv l++
  lcl|FitnessBrowser__azobra:AZOBR_RS10920 361 VQYHPEASPGPQDSHYLFDRFVALMD 386
                                               **********************9985 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: 10.95
//
[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