Alignments for a candidate for paaJ2 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>FitnessBrowser__Koxy:BWI76_RS16135
          Length = 400

 Score =  617 bits (1590), Expect = 0.0
 Identities = 310/399 (77%), Positives = 352/399 (88%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +A ICDA+RTPFGR+GG L  +RADDLAA P+++L+ERNPG+D +R++D++YGCANQAGE
Sbjct: 3   QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARMA LLAGLP +VPGSTVNRLCGSSLDA+G+AARAIKSGE QLMIAGGVESM+R
Sbjct: 63  DNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSR 122

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKAESAF+R+  + DTTIGWRF+NP MKA YG+DSMPETAENVA DF I+RADQD
Sbjct: 123 APFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYGVDSMPETAENVADDFAISRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQ R AAAQ AG FA E+  +++PQ+KG+PL+ + DEHPR  TT   LA+L+GVV
Sbjct: 183 AFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPR-TTTAEALARLRGVV 241

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
           RPDGTVTAGNASGVNDGACALLLAS +A     L+P ARV+G+ATAGVAPRIMGFGPAPA
Sbjct: 242 RPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPAPA 301

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRKVLAQ GLTL QMDVIELNEAFAAQ LAV RDLGLPDDAA+VNPNGGAIA+GHPLGAS
Sbjct: 302 VRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLGAS 361

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           G RL  TA  QL R+GGRYALCTMCIGVGQGIAL+IERV
Sbjct: 362 GGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 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: 594
Number of extensions: 16
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 BWI76_RS16135 BWI76_RS16135 (acetyl-CoA acetyltransferase)
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.27241.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.3e-222  724.1   9.8   2.6e-222  723.9   9.8    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS16135  BWI76_RS16135 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS16135  BWI76_RS16135 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.9   9.8  2.6e-222  2.6e-222       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 723.9 bits;  conditional E-value: 2.6e-222
                               TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaal 72 
                                             +++i+da+rtp+Gr+gG+l+++raddlaa+plkall+rnp ld a iddvi+GcanqaGednrnvarma+l
  lcl|FitnessBrowser__Koxy:BWI76_RS16135   3 QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGEDNRNVARMALL 73 
                                             79********************************************************************* PP

                               TIGR02430  73 laGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledtt 143
                                             laGlp+svpg+tvnrlcgs+lda+g+aaraik+Ge++l+iaGGvesmsrapfv+Gka+safsr+ ++edtt
  lcl|FitnessBrowser__Koxy:BWI76_RS16135  74 LAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSRAPFVMGKAESAFSRTMRMEDTT 144
                                             *********************************************************************** PP

                               TIGR02430 144 iGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkG 214
                                             iGwrf+np++kalyGvdsmpetaenva++f++sr+dqdafalrsq rtaaaq++G fa+e++ v+++q+kG
  lcl|FitnessBrowser__Koxy:BWI76_RS16135 145 IGWRFINPQMKALYGVDSMPETAENVADDFAISRADQDAFALRSQLRTAAAQEAGRFADELIAVSVPQRKG 215
                                             *********************************************************************** PP

                               TIGR02430 215 eetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaa 285
                                             e+  +++deh+r  tt eala+l++vvr+dgtvtaGnasGvndGa+alllase+a+++++l+p ar++++a
  lcl|FitnessBrowser__Koxy:BWI76_RS16135 216 EPLLFSRDEHPR-TTTAEALARLRGVVRPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVA 285
                                             ************.89******************************************************** PP

                               TIGR02430 286 saGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGh 356
                                             +aGv+pr+mG+gp+pav+k+la++gl+l ++dvielneafaaqalav+r+lgl+dd+a vnpnGGaialGh
  lcl|FitnessBrowser__Koxy:BWI76_RS16135 286 TAGVAPRIMGFGPAPAVRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGH 356
                                             *********************************************************************** PP

                               TIGR02430 357 plGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                             plGasG rl++ta +ql+++ggryal+t+ciGvGqGial+ierv
  lcl|FitnessBrowser__Koxy:BWI76_RS16135 357 PLGASGGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.28
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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