GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pseudomonas stutzeri RCH2

Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate GFF485 Psest_0490 Threonine dehydrogenase and related Zn-dependent dehydrogenases

Query= SwissProt::Q0KDL6
         (366 letters)



>FitnessBrowser__psRCH2:GFF485
          Length = 357

 Score =  598 bits (1542), Expect = e-176
 Identities = 297/363 (81%), Positives = 321/363 (88%), Gaps = 7/363 (1%)

Query: 3   AMMKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTVGH 62
           AMMKAAVFVEPGRIEL DKPIP+IGPNDAL+RITTTTICGTDVHILKGEYPVA GLT+GH
Sbjct: 2   AMMKAAVFVEPGRIELQDKPIPEIGPNDALLRITTTTICGTDVHILKGEYPVAAGLTIGH 61

Query: 63  EPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHGYK 122
           EPVG+IEKLGS V GY+EGQRVIAGAICP+F SYA QDG+ SQDG        C CHGYK
Sbjct: 62  EPVGVIEKLGSNVKGYQEGQRVIAGAICPSFTSYACQDGLPSQDGG-------CSCHGYK 114

Query: 123 ATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENANIR 182
              GWRFGN IDGTQAEYVLVPDAQANL P+PDGLTDEQVLMCPDIMSTGF GAE ANI+
Sbjct: 115 PMGGWRFGNTIDGTQAEYVLVPDAQANLAPVPDGLTDEQVLMCPDIMSTGFAGAEAANIK 174

Query: 183 IGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDVVD 242
           IGD V +FAQGPIGLCATAGA+L GA+TIIA+DG D RL+IARKMGADV LNFRN DVVD
Sbjct: 175 IGDIVVIFAQGPIGLCATAGAKLRGASTIIAVDGVDARLDIARKMGADVTLNFRNVDVVD 234

Query: 243 EVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGLGD 302
           EV+KLT GRG DASIEALG Q+TFE +LRVLKPGGTLSSLGVYSSDLTIPL AF AGLGD
Sbjct: 235 EVLKLTSGRGADASIEALGLQSTFESALRVLKPGGTLSSLGVYSSDLTIPLGAFHAGLGD 294

Query: 303 HKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLKIA 362
           +KI T+LCPGGKERMRRL+NV+ SGRVDLG LVTH+Y LD+I  AYDLFANQRDGVLK+A
Sbjct: 295 NKIVTSLCPGGKERMRRLLNVVASGRVDLGLLVTHKYALDNITDAYDLFANQRDGVLKVA 354

Query: 363 IKP 365
           IKP
Sbjct: 355 IKP 357


Lambda     K      H
   0.320    0.138    0.408 

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: 590
Number of extensions: 15
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: 366
Length of database: 357
Length adjustment: 29
Effective length of query: 337
Effective length of database: 328
Effective search space:   110536
Effective search space used:   110536
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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