Alignments for a candidate for paaJ2 in Klebsiella variicola At-22

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Klebsiella variicola At-22

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_008805052.1 KVAR_RS13980 3-oxoadipyl-CoA thiolase

Query= uniprot:D8ITH5
         (401 letters)



>NCBI__GCF_000025465.1:WP_008805052.1
          Length = 400

 Score =  614 bits (1584), Expect = e-180
 Identities = 309/399 (77%), Positives = 352/399 (88%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +A ICDA+RTPFGR+GG L  +RADDLAA P+++L+ERNPG+D SR++D+++GCANQAGE
Sbjct: 3   QAFICDAVRTPFGRFGGTLATMRADDLAALPLKALLERNPGLDPSRIDDVIFGCANQAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARMA LLAGLP +VPGST+NRLCGSSLDA+G+AARAIKSGE QLMIAGGVESM+R
Sbjct: 63  DNRNVARMALLLAGLPESVPGSTINRLCGSSLDAIGVAARAIKSGETQLMIAGGVESMSR 122

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKAESAF+RS  + DTTIGWRF+NP MKA YG+ SMPETAENVA +F I+RADQD
Sbjct: 123 APFVMGKAESAFSRSMQMEDTTIGWRFINPQMKALYGVHSMPETAENVADEFAISRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQ R AAAQ AG FA E+  + +PQ+KG+PL+ + DEHPR  T+L  LAKL+GVV
Sbjct: 183 AFALRSQLRTAAAQEAGRFADELIAVQVPQRKGEPLLFSRDEHPR-STSLEALAKLRGVV 241

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
           R DG+VTAGNASGVNDGACALLLAS  A   + L+P ARV+G+ATAGVAPRIMGFGPAPA
Sbjct: 242 RADGSVTAGNASGVNDGACALLLASETALAAHDLQPLARVVGVATAGVAPRIMGFGPAPA 301

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRKVLAQ GLTLAQMDVIELNEAFAAQ LAV RDLGLPDDAAHVNPNGGAIA+GHPLGAS
Sbjct: 302 VRKVLAQTGLTLAQMDVIELNEAFAAQALAVTRDLGLPDDAAHVNPNGGAIALGHPLGAS 361

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           G RL  TA  QL+R+GGRYALCTMCIGVGQGIAL+IERV
Sbjct: 362 GGRLAMTAAYQLKRTGGRYALCTMCIGVGQGIALIIERV 400


Lambda     K      H
   0.320    0.135    0.394 

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: 579
Number of extensions: 15
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: 401
Length of database: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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: 50 (23.9 bits)

Align candidate WP_008805052.1 KVAR_RS13980 (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.4017327.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-223  726.2   9.6     6e-223  726.0   9.6    1.0  1  NCBI__GCF_000025465.1:WP_008805052.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025465.1:WP_008805052.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  726.0   9.6    6e-223    6e-223       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 726.0 bits;  conditional E-value: 6e-223
                             TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 
                                           +++i+da+rtp+Gr+gG+l+++raddlaa+plkall+rnp ld + iddvi+GcanqaGednrnvarma+lla
  NCBI__GCF_000025465.1:WP_008805052.1   3 QAFICDAVRTPFGRFGGTLATMRADDLAALPLKALLERNPGLDPSRIDDVIFGCANQAGEDNRNVARMALLLA 75 
                                           79*********************************************************************** PP

                             TIGR02430  75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147
                                           Glp+svpg+t+nrlcgs+lda+g+aaraik+Ge++l+iaGGvesmsrapfv+Gka+safsrs ++edttiGwr
  NCBI__GCF_000025465.1:WP_008805052.1  76 GLPESVPGSTINRLCGSSLDAIGVAARAIKSGETQLMIAGGVESMSRAPFVMGKAESAFSRSMQMEDTTIGWR 148
                                           ************************************************************************* PP

                             TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220
                                           f+np++kalyGv+smpetaenva+ef++sr+dqdafalrsq rtaaaq++G fa+e++ v+++q+kGe+  ++
  NCBI__GCF_000025465.1:WP_008805052.1 149 FINPQMKALYGVHSMPETAENVADEFAISRADQDAFALRSQLRTAAAQEAGRFADELIAVQVPQRKGEPLLFS 221
                                           ************************************************************************* PP

                             TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293
                                           +deh+r +t+lealakl++vvr+dg+vtaGnasGvndGa+alllase a+++h+l+p ar++++a+aGv+pr+
  NCBI__GCF_000025465.1:WP_008805052.1 222 RDEHPR-STSLEALAKLRGVVRADGSVTAGNASGVNDGACALLLASETALAAHDLQPLARVVGVATAGVAPRI 293
                                           ******.9***************************************************************** PP

                             TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366
                                           mG+gp+pav+k+la++gl+l+++dvielneafaaqalav+r+lgl+dd+a+vnpnGGaialGhplGasG rl+
  NCBI__GCF_000025465.1:WP_008805052.1 294 MGFGPAPAVRKVLAQTGLTLAQMDVIELNEAFAAQALAVTRDLGLPDDAAHVNPNGGAIALGHPLGASGGRLA 366
                                           ************************************************************************* PP

                             TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400
                                           +ta +ql+++ggryal+t+ciGvGqGial+ierv
  NCBI__GCF_000025465.1:WP_008805052.1 367 MTAAYQLKRTGGRYALCTMCIGVGQGIALIIERV 400
                                           *********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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: 10.77
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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