Alignments for a candidate for pcaB in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for pcaB in Azospirillum brasilense Sp245

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate AZOBR_RS28125 AZOBR_RS28125 3-carboxy-cis cis-muconate cycloisomerase

Query= curated2:Q9I6Q8
         (459 letters)



>FitnessBrowser__azobra:AZOBR_RS28125
          Length = 453

 Score =  384 bits (986), Expect = e-111
 Identities = 217/445 (48%), Positives = 272/445 (61%), Gaps = 3/445 (0%)

Query: 2   SDVPANQLFDAYFMAAPMRAVFSDRGRLQGMLDFEAALARAEARTGVVPATAVAPIEAAC 61
           S +  + +F   F    MRAV+SD  R +  LD EAALAR + R G++P  A   I A C
Sbjct: 3   STIIDSAIFGDIFSTPAMRAVWSDENRTRKYLDIEAALARVQGRLGIIPQEAADEIVANC 62

Query: 62  RAELYDPLALAEAVATAGNSAIPLVKALGRQVAAGDAEAERYVHLGATSQDAMDSGLVLQ 121
             +  D   L       G   + +V  L    A        Y H GAT+QD  D+  VLQ
Sbjct: 63  SLDRIDMATLKAQTERIGYPVLGVVSQLN---ALCRDRLGEYCHWGATTQDITDTATVLQ 119

Query: 122 LRRALALLEQDLQRLAEVLADQAERHADTPLAGRTWLQHATPVTLGMKLAGLLGALTRHR 181
           +R AL L+++DL  L+  LA  A+RH DTP+ GR+ LQ A PVT G K+AGLL A+ RHR
Sbjct: 120 MREALNLVDEDLAGLSAALATLAKRHRDTPMIGRSNLQQAVPVTFGYKMAGLLSAVERHR 179

Query: 182 QRLRELRPRLLVLQFGGASGTLAALGEQALPVAAALAEELGLALPEQPWHTQRDRLVEFA 241
           +RL +LRPR+L+ +F GASGTLA+L   A+   A L EEL LA P   WHT RD + E  
Sbjct: 180 ERLAQLRPRVLMGEFAGASGTLASLEHGAMETQAGLMEELDLAQPVIAWHTIRDTIAEVG 239

Query: 242 SVLGLVAGSLGKFGRDVSLLMQTEAGEVFEPAGAGRGGSSTMPHKRNPVSSAVLIAAATR 301
             LGLV G+LGK   DV L+MQTE GEV+EP   GRG SSTMP KRNP+SS  + A+ + 
Sbjct: 240 CFLGLVGGTLGKLSMDVKLMMQTEVGEVYEPFAHGRGSSSTMPQKRNPISSCYIHASISV 299

Query: 302 APGLVSTLFAAMPQEHERSLGLWHAEWETLPELCCLVAGALQQAIGLLEGLEVDAQRMRR 361
                + L  AM  +HERS G W  EW  LPE  CL+AGAL+QA  ++ GLEVDA+RMR 
Sbjct: 300 LRQHTAALLDAMVADHERSTGPWEIEWIVLPEAFCLLAGALKQARFVVSGLEVDAERMRA 359

Query: 362 NLGLTHGLVLAEAVSIALARRIGREAAHHLVEQCCRRAVEQRRELRAVLGEEARVSAELS 421
           NL +T+GLV +EAV + L R IGRE AH LV   CR AV Q R L  +L E   +SA LS
Sbjct: 360 NLEMTNGLVASEAVMMGLGRHIGREYAHDLVYDLCREAVRQNRPLLDLLAETPEISACLS 419

Query: 422 GDELDRLLDPAHYLGQARAWVERAL 446
             EL +L DPA+YLGQ+   V+R L
Sbjct: 420 RAELAKLCDPANYLGQSGVMVDRVL 444


Lambda     K      H
   0.320    0.133    0.386 

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: 507
Number of extensions: 20
Number of successful extensions: 2
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: 459
Length of database: 453
Length adjustment: 33
Effective length of query: 426
Effective length of database: 420
Effective search space:   178920
Effective search space used:   178920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS28125 AZOBR_RS28125 (3-carboxy-cis cis-muconate cycloisomerase)
to HMM TIGR02426 (pcaB: 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2))

# 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.carbon/TIGR02426.hmm
# target sequence database:        /tmp/gapView.25139.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02426  [M=338]
Accession:   TIGR02426
Description: protocat_pcaB: 3-carboxy-cis,cis-muconate cycloisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.8e-112  359.9   2.9   7.5e-112  359.5   2.9    1.1  1  lcl|FitnessBrowser__azobra:AZOBR_RS28125  AZOBR_RS28125 3-carboxy-cis cis-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS28125  AZOBR_RS28125 3-carboxy-cis cis-muconate cycloisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.5   2.9  7.5e-112  7.5e-112       3     338 .]      12     350 ..      10     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 359.5 bits;  conditional E-value: 7.5e-112
                                 TIGR02426   3 dglfgdseaaelfsdrarlramldvEaalaraqadvGlipaeaaeaiaaaaaelalDlealaeaaaeag 71 
                                                ++f+++++++++sd+ r r  ld+Eaalar+q+++G+ip+eaa++i+a ++  ++D+++l++++++ g
  lcl|FitnessBrowser__azobra:AZOBR_RS28125  12 GDIFSTPAMRAVWSDENRTRKYLDIEAALARVQGRLGIIPQEAADEIVANCSLDRIDMATLKAQTERIG 80 
                                               689****************************************************************** PP

                                 TIGR02426  72 nvviplvkalrkavaeeaaryvHlGaTSQDviDTalmLqlrdaldllladlerlaeaLaelaarhrdtp 140
                                                +v+++v +l++   +  ++y H+GaT QD+ DTa++Lq+r+al+l+++dl+ l++aLa+la+rhrdtp
  lcl|FitnessBrowser__azobra:AZOBR_RS28125  81 YPVLGVVSQLNALCRDRLGEYCHWGATTQDITDTATVLQMREALNLVDEDLAGLSAALATLAKRHRDTP 149
                                               ********************************************************************* PP

                                 TIGR02426 141 ltarTllQqAvpttvglkaagwlaavlrardrlealrtealalqfGGAaGtlaalekkglavaealAae 209
                                               +++r  lQqAvp+t+g k+ag l+av+r+r+rl++lr ++l  +f GA+Gtla+le+ +++ ++ l +e
  lcl|FitnessBrowser__azobra:AZOBR_RS28125 150 MIGRSNLQQAVPVTFGYKMAGLLSAVERHRERLAQLRPRVLMGEFAGASGTLASLEHGAMETQAGLMEE 218
                                               ********************************************************************* PP

                                 TIGR02426 210 lgLeapalpWhtqrdriaelaaaLalvagalgkiaqDvallaqtevgevle..agg.GGSSampHKrNP 275
                                               l+L++p   Wht rd+iae+++ L+lv g+lgk++ Dv l++qtevgev e  a g G SS+mp KrNP
  lcl|FitnessBrowser__azobra:AZOBR_RS28125 219 LDLAQPVIAWHTIRDTIAEVGCFLGLVGGTLGKLSMDVKLMMQTEVGEVYEpfAHGrGSSSTMPQKRNP 287
                                               ***************************************************87666899********** PP

                                 TIGR02426 276 vaaevlaaaarrapglvatLfaalaqedeRsaggWhaeWetLrelvaltagalrqaaellegl 338
                                               + +  + a      +  a+L++a+++ +eRs+g W++eW +L+e ++l agal+qa+ ++ gl
  lcl|FitnessBrowser__azobra:AZOBR_RS28125 288 ISSCYIHASISVLRQHTAALLDAMVADHERSTGPWEIEWIVLPEAFCLLAGALKQARFVVSGL 350
                                               ********9999*********************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (338 nodes)
Target sequences:                          1  (453 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: 10.45
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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

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 catabolism of small carbon sources