GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Chryseobacterium arthrosphaerae CC-VM-7

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_065401082.1 BBI00_RS22490 3-oxoadipyl-CoA thiolase

Query= uniprot:B2SYZ2
         (400 letters)



>NCBI__GCF_001684965.1:WP_065401082.1
          Length = 401

 Score =  494 bits (1271), Expect = e-144
 Identities = 245/401 (61%), Positives = 311/401 (77%), Gaps = 1/401 (0%)

Query: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60
           MN+ +I D +RTPI +  G L +VRADDL A+ IK ++ RNP V    ++DVI+GCANQA
Sbjct: 1   MNNVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQA 60

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           GEDNRNVARM  LLAGLP +  G T+NRLC SGM AV  A R+I +GE  + IAGGVE M
Sbjct: 61  GEDNRNVARMGLLLAGLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHM 120

Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180
           TR+P+VM K  +AF R + ++DTT GWRFINP MK  YGVD M ETAEN+A    +SR D
Sbjct: 121 TRSPYVMSKPGAAFGRDSQMFDTTFGWRFINPKMKEMYGVDGMGETAENLADMHHISRED 180

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRE-TSLESLGKLKG 239
           QD FAL SQQKA +AQ+ G LA+EIV VEI Q+KG+PV    DE  +  +S+E LGKL+ 
Sbjct: 181 QDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFEKDEFIKPGSSMEGLGKLRP 240

Query: 240 VVRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPA 299
             R +G+VTAGNASG+NDGA AL+LA+++A  +YGL+ +AR++G + AGVEPRIMGIGP 
Sbjct: 241 AFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRIMGIGPV 300

Query: 300 PATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLG 359
            ATQKLLK+L ++LE +D+IELNEAFA+Q LAV RTLGL+DDD R+NPNGGAIA+GHPLG
Sbjct: 301 EATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPLG 360

Query: 360 ASGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400
            SGAR+I +A  +L++ N ++ALCT+CIGVGQG A+VIE++
Sbjct: 361 VSGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401


Lambda     K      H
   0.318    0.135    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: 478
Number of extensions: 18
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: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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 WP_065401082.1 BBI00_RS22490 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.3032045.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-198  644.2   1.5   4.6e-198  644.1   1.5    1.0  1  NCBI__GCF_001684965.1:WP_065401082.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001684965.1:WP_065401082.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.1   1.5  4.6e-198  4.6e-198       2     400 .]       3     401 .]       2     401 .] 1.00

  Alignments for each domain:
  == domain 1  score: 644.1 bits;  conditional E-value: 4.6e-198
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           +vyi+d +rtpi +  G+ls+vraddlaa+ +k+++arnp++ ++ i+dvi+GcanqaGednrnvarm +lla
  NCBI__GCF_001684965.1:WP_065401082.1   3 NVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQAGEDNRNVARMGLLLA 75 
                                           89*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp ++ g tvnrlc+sg+ a++ a+r+i++Ge ++ iaGGve m+r+p+v+ k  +af+r+ +++dtt+Gwr
  NCBI__GCF_001684965.1:WP_065401082.1  76 GLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHMTRSPYVMSKPGAAFGRDSQMFDTTFGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           f+npk+k++yGvd m+etaen+a+ + +sredqd+fal sqq++++aq++G +aeeiv+vei+q+kGe+++++
  NCBI__GCF_001684965.1:WP_065401082.1 149 FINPKMKEMYGVDGMGETAENLADMHHISREDQDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFE 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           kde  ++ +++e+l kl++ +r++gtvtaGnasG+ndGaaal+laseeavk++gl+p+aril+++ aGvepr+
  NCBI__GCF_001684965.1:WP_065401082.1 222 KDEFIKPGSSMEGLGKLRPAFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRI 294
                                           ************************************************************************* PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gpv a++kll+r++lsled+d+ielneafaaqalav+r lgl+ddd+r+npnGGaia+GhplG+sGar++
  NCBI__GCF_001684965.1:WP_065401082.1 295 MGIGPVEATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPLGVSGARII 367
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                            +a  +l+k++++yal+tlciGvGqG a+vie+v
  NCBI__GCF_001684965.1:WP_065401082.1 368 GSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 401
                                           ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (401 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.16
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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