Alignments for a candidate for paaZ1 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ1 in Klebsiella michiganensis M5al

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate BWI76_RS13085 BWI76_RS13085 bifunctional oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__Koxy:BWI76_RS13085
          Length = 681

 Score = 1193 bits (3087), Expect = 0.0
 Identities = 592/679 (87%), Positives = 632/679 (93%)

Query: 1   MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60
           MQQLAS+LSGTWQ+GRG +R IHHAISG+ALWEVTS GLDMA AR+FAIE+G  AL+AMT
Sbjct: 1   MQQLASYLSGTWQTGRGHARTIHHAISGDALWEVTSAGLDMAQARRFAIERGGKALQAMT 60

Query: 61  FIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD 120
           FIER+AMLKAVA+HLL +K   YA+SA+TGATR+DSWVDIEGGIGTLFTYA LGSRELPD
Sbjct: 61  FIERSAMLKAVARHLLEQKAALYAISAETGATRSDSWVDIEGGIGTLFTYAGLGSRELPD 120

Query: 121 DTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAII 180
           DTLWPEDELIPLSK+GGFAARH+LTSKSGVAVHINAFNFPCWGMLEKLAPTWL GMPAII
Sbjct: 121 DTLWPEDELIPLSKQGGFAARHVLTSKSGVAVHINAFNFPCWGMLEKLAPTWLAGMPAII 180

Query: 181 KPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQML 240
           KPATATAQLTQAMVK IVDSGLVPEGAISLICG AGDLLDHLDSQDVVTFTGSA TGQ L
Sbjct: 181 KPATATAQLTQAMVKMIVDSGLVPEGAISLICGGAGDLLDHLDSQDVVTFTGSARTGQQL 240

Query: 241 RVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRR 300
           RV PN+VAKSIPFTMEADSLNCCVLG+DVTP+QPEFALFIREVVREMT KAGQKCTAIRR
Sbjct: 241 RVHPNLVAKSIPFTMEADSLNCCVLGDDVTPEQPEFALFIREVVREMTAKAGQKCTAIRR 300

Query: 301 IIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEI 360
           IIVPQA V AVSDAL+ARLQ VVVGDPAQEGVKMGALVN EQR DVQ+ VN L+AAGC++
Sbjct: 301 IIVPQAQVKAVSDALIARLQNVVVGDPAQEGVKMGALVNYEQRQDVQDNVNRLVAAGCDV 360

Query: 361 RLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAGG 420
            LGGQADL AAGAFFPPTLL+CPQPDETPAVHA EAFGPVATLMP QN  HA+ LA AG 
Sbjct: 361 LLGGQADLRAAGAFFPPTLLFCPQPDETPAVHAIEAFGPVATLMPYQNIEHAMSLARAGE 420

Query: 421 GSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAGG 480
           GSLAGTLVTA  ++AR FI  AARTHGRIQILNE S+ ESTGHGSPLPQLVHGGPGRAGG
Sbjct: 421 GSLAGTLVTASGELARAFILGAARTHGRIQILNESSSAESTGHGSPLPQLVHGGPGRAGG 480

Query: 481 GEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSL 540
           GEELGGLRAVKHYMQRTA+QGSPTMLAAI +QWVRGA+V EDRIHPFRKYFEE+QPGDSL
Sbjct: 481 GEELGGLRAVKHYMQRTAIQGSPTMLAAIGQQWVRGAEVVEDRIHPFRKYFEEIQPGDSL 540

Query: 541 LTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDAGV 600
           LTPRRT+TEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYF++SAAAGLFVDAGV
Sbjct: 541 LTPRRTLTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFLISAAAGLFVDAGV 600

Query: 601 GPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQHQ 660
           GPVIANYG+E+LRFIEPVKPGDTIQVRLTCKRKT+K+QRSAEEK TGVVEWAVE+FNQHQ
Sbjct: 601 GPVIANYGMENLRFIEPVKPGDTIQVRLTCKRKTVKRQRSAEEKATGVVEWAVEIFNQHQ 660

Query: 661 TPVALYSILTLVARQHGDF 679
             VALYSILTLVARQ GDF
Sbjct: 661 QAVALYSILTLVARQQGDF 679


Lambda     K      H
   0.319    0.134    0.395 

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: 1428
Number of extensions: 31
Number of successful extensions: 1
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: 681
Length of database: 681
Length adjustment: 39
Effective length of query: 642
Effective length of database: 642
Effective search space:   412164
Effective search space used:   412164
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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

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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