Alignments for a candidate for paaZ2 in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Paraburkholderia bryophila 376MFSha3.1

Align 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC 1.2.1.91) (characterized)
to candidate H281DRAFT_05724 H281DRAFT_05724 phenylacetic acid degradation protein paaN

Query= reanno::BFirm:BPHYT_RS17340
         (566 letters)



>FitnessBrowser__Burk376:H281DRAFT_05724
          Length = 566

 Score = 1060 bits (2741), Expect = 0.0
 Identities = 527/566 (93%), Positives = 543/566 (95%)

Query: 1   MTHPLFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQL 60
           MTHPLFTKHEDTLQKAL AVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATF+L
Sbjct: 1   MTHPLFTKHEDTLQKALAAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFEL 60

Query: 61  DQPSTGETVGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEILA 120
           DQPSTGETVG EVSPFGFPLG+RYPK++P AL+AAAA AQRDWRAAGPQAWIGV LEILA
Sbjct: 61  DQPSTGETVGTEVSPFGFPLGIRYPKSDPDALLAAAAEAQRDWRAAGPQAWIGVSLEILA 120

Query: 121 RVNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEKPQ 180
           R+NRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIP D HWEKPQ
Sbjct: 121 RLNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPADAHWEKPQ 180

Query: 181 GKNPPLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILPLA 240
           GKNPPLAM KRYT+VPRGT LVLGCCTFPTWNGYPGLFADLATGN VIVKPHPGAILPLA
Sbjct: 181 GKNPPLAMQKRYTIVPRGTALVLGCCTFPTWNGYPGLFADLATGNAVIVKPHPGAILPLA 240

Query: 241 LTVRIARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLERN 300
           +TVRIARDVLREAGFDPNVVTLLATEPNDGA+VQ LA+RPEIKLIDFTGSTQNGTWLERN
Sbjct: 241 VTVRIARDVLREAGFDPNVVTLLATEPNDGAIVQSLAVRPEIKLIDFTGSTQNGTWLERN 300

Query: 301 AHQAQVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRTAE 360
           AHQAQVYTEKAGVNQIVIDS DDIKA ARN+AFSLALYSGQMCTAPQNIYVPR GI+TA+
Sbjct: 301 AHQAQVYTEKAGVNQIVIDSADDIKAVARNIAFSLALYSGQMCTAPQNIYVPRDGIQTAD 360

Query: 361 GTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTLEH 420
           GTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGV QR+DEAA LGRVLVES  LEH
Sbjct: 361 GTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVAQRVDEAATLGRVLVESQALEH 420

Query: 421 PAFAGARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGALT 480
           PAFAGARVRTPLVLQLDAATD  QFTKEWFGPISFVIATDSTA SLDLAG IA+EHGALT
Sbjct: 421 PAFAGARVRTPLVLQLDAATDGEQFTKEWFGPISFVIATDSTAHSLDLAGTIAAEHGALT 480

Query: 481 LSVYSTDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADA 540
           LSVYSTDEAVLD AHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADA
Sbjct: 481 LSVYSTDEAVLDQAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALADA 540

Query: 541 AFVANRFRVVQSRVHVEPKAAPAVAG 566
           AFVANRFRV+QSRVHVEPKAAPAVAG
Sbjct: 541 AFVANRFRVIQSRVHVEPKAAPAVAG 566


Lambda     K      H
   0.318    0.133    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: 1077
Number of extensions: 27
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: 566
Length of database: 566
Length adjustment: 36
Effective length of query: 530
Effective length of database: 530
Effective search space:   280900
Effective search space used:   280900
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. 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 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