Alignments for a candidate for ketodeoxyribonate-cleavage in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ketodeoxyribonate-cleavage in Herbaspirillum seropedicae SmR1

Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate HSERO_RS17240 HSERO_RS17240 hypothetical protein

Query= reanno::WCS417:GFF1426
         (310 letters)



>FitnessBrowser__HerbieS:HSERO_RS17240
          Length = 310

 Score =  494 bits (1272), Expect = e-144
 Identities = 236/310 (76%), Positives = 271/310 (87%)

Query: 1   MSKNRPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRP 60
           M++ R VIITCAVTGAIHTPSMSP+LP+T ++I D A+ AAEAGAAIVHLHARDP +G+P
Sbjct: 1   MAQPRKVIITCAVTGAIHTPSMSPYLPVTPEQIRDEALAAAEAGAAIVHLHARDPGNGKP 60

Query: 61  SQDPALFAEFLPQIKAASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGL 120
           +QDP  F +FLPQIKA S+VVIN+TTGGAPTMGVEERLQP +Q KPE+ASLNMGSMNFGL
Sbjct: 61  TQDPDAFRKFLPQIKARSNVVINLTTGGAPTMGVEERLQPALQLKPEVASLNMGSMNFGL 120

Query: 121 YEMLNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYT 180
           YEMLNRF DFK+DWE+PYL  SDDRIFRNTF+DI +IL +C+ N+TRFEIECYDIGHLYT
Sbjct: 121 YEMLNRFKDFKYDWEQPYLAGSDDRIFRNTFKDIAYILESCSANQTRFEIECYDIGHLYT 180

Query: 181 AAHFLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLFGSDYVWSILGAGRGQI 240
           AAHF++RGL+KPP  IQSVFGLRGGIG   ED+ HM+RTADRLFG DY WS+LGAGRGQI
Sbjct: 181 AAHFIDRGLIKPPFLIQSVFGLRGGIGNDVEDVMHMKRTADRLFGQDYFWSVLGAGRGQI 240

Query: 241 PLATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREIL 300
           P+ATM  +MG + RVGLEDSLWDGPGKLA SNADQVRRIRTVIEAL   VA+P++AR +L
Sbjct: 241 PIATMAAAMGGHTRVGLEDSLWDGPGKLARSNADQVRRIRTVIEALSLEVASPEDARAML 300

Query: 301 GLKGRDQVNF 310
            LKG DQV F
Sbjct: 301 KLKGGDQVGF 310


Lambda     K      H
   0.321    0.138    0.416 

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: 404
Number of extensions: 7
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: 310
Length of database: 310
Length adjustment: 27
Effective length of query: 283
Effective length of database: 283
Effective search space:    80089
Effective search space used:    80089
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 (21.9 bits)
S2: 48 (23.1 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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