Alignments for a candidate for put1 in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_018233000.1 THITHI_RS0110235 FAD-dependent oxidoreductase

Query= BRENDA::Q5JFG2
         (385 letters)



>NCBI__GCF_000378965.1:WP_018233000.1
          Length = 412

 Score =  179 bits (453), Expect = 2e-49
 Identities = 117/386 (30%), Positives = 195/386 (50%), Gaps = 12/386 (3%)

Query: 1   MKSEAKTVIIGGGIIGLSIAYNLAK-LGESDIVVLEKGYLGNGSTFRCGTGIRQQFGDEA 59
           ++     VIIGGG  GL+ AY LA+  G +++ VLE+GY+G G+T R  T +R  +    
Sbjct: 25  LRDSYDVVIIGGGGHGLACAYYLARDHGITNVAVLEQGYIGGGNTGRNTTIVRSNYLTPE 84

Query: 60  NIRMMKRSVELWKGLKEELGYDVEFTQSGYLFLIYSEEELEAFNNNVRLQNRFGVPSRII 119
            ++    S+ L++ L E+   ++ +++ G+  L +++  +        +   FG+ S ++
Sbjct: 85  GVKFYDESIRLFRDLAEDFDLNIFYSERGHFTLAHTDAAVRTMRWRAEVNKHFGIDSELV 144

Query: 120 TPEEAKEIVPPLNTD----GVIAAAWNHTDGKANPFKAV-FAYANAAKRLGVEIYEYTEA 174
             E   + VP L+ D      +  A  H  G      AV + Y   A R GVEI++ T  
Sbjct: 145 DREFIADAVPMLDLDCGGEHPVLGALYHVPGAVVRHDAVAWGYGRGADRRGVEIHQKTRV 204

Query: 175 KDIKVEDGKIKAVVTNRGEIRTGRVINAANAWAPLINKMAGVPIKIPIEPYKHQSVKTEP 234
             I+VE G++  V T++G ++TGRVI+      P I  M G+   I I P   Q+  TEP
Sbjct: 205 TGIRVEQGRVTGVETDKGFVKTGRVISMVAGSTPRITDMVGITTPIVIHPL--QACVTEP 262

Query: 235 IKPGQIEPMVISFKHGGVYMTQEANQGGVIGGYGLKYGPTYDITPTYDFLRGVSYRFAQI 294
           +KP     +V    H  VY++Q +++G ++ G  L     +    T DF+ G++ +   +
Sbjct: 263 MKPWLDTIIVSGSLH--VYVSQ-SSRGELVMGAALDPAILHSTRSTLDFVEGLADQMLDL 319

Query: 295 IPALKYVNIIRVWGGFYAETPDHNAAIGRINEIDEFYIAAGFSGHGFMLAPVVGEALAEL 354
            P L    ++R W G    TPD    +GR   ID FYI AG+   GF   PV G+ +A  
Sbjct: 320 FPFLSRAKVMRQWAGMADMTPDFAPIMGR-TAIDGFYIDAGWGTWGFKATPVSGKTMAWT 378

Query: 355 IVDGKTDKPLDFYDPYRFERGELRGQ 380
           + + +  + ++ +   RF+R EL G+
Sbjct: 379 VANDRDHELIEPFSLARFDRFELVGE 404


Lambda     K      H
   0.318    0.139    0.412 

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: 383
Number of extensions: 22
Number of successful extensions: 5
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: 385
Length of database: 412
Length adjustment: 31
Effective length of query: 354
Effective length of database: 381
Effective search space:   134874
Effective search space used:   134874
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. 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 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