GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pseudomonas fluorescens FW300-N1B4

Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate Pf1N1B4_2673 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= reanno::psRCH2:GFF2231
         (506 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2673
          Length = 506

 Score =  904 bits (2335), Expect = 0.0
 Identities = 437/506 (86%), Positives = 473/506 (93%)

Query: 1   MIYAQPGTPGAVVSFKPRYGNYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEK 60
           M YA PGT GA+VSFK +YGNYIGGEFV PVKG+YF NTSPVNG+ IAEFPRS AEDIEK
Sbjct: 1   MRYAHPGTEGAIVSFKSKYGNYIGGEFVAPVKGQYFTNTSPVNGQPIAEFPRSTAEDIEK 60

Query: 61  ALDAAHAAADAWGKTSVQDRALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPL 120
           ALDAAHAAADAWG TS Q R+L+LLKIADRIE NLE LA+ E+WDNGKAVRETLNAD+PL
Sbjct: 61  ALDAAHAAADAWGATSAQARSLVLLKIADRIEQNLELLAITESWDNGKAVRETLNADIPL 120

Query: 121 AADHFRYFAGCIRAQEGSAAEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALA 180
           AADHFRYFAGCIRAQEGSAAEI+ +T AYH HEPLGVVGQIIPWNFP+LMAAWKLAPALA
Sbjct: 121 AADHFRYFAGCIRAQEGSAAEIDGNTVAYHIHEPLGVVGQIIPWNFPILMAAWKLAPALA 180

Query: 181 AGNCIVLKPAEQTPLSIMVFIEVVGDLLPPGVLNIVQGFGREAGQALATSTRIAKIAFTG 240
           AGNCIVLKPAEQTPL I V +E++GDLLPPGVLN+VQGFG+EAG+ALATS RIAKIAFTG
Sbjct: 181 AGNCIVLKPAEQTPLGITVLMELIGDLLPPGVLNVVQGFGKEAGEALATSKRIAKIAFTG 240

Query: 241 STPVGSHIMRCAAENIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEV 300
           STPVGSHIM+CAAENIIPSTVELGGKSPNIFFEDIM AEP+FIEKAAEGLVLAFFNQGEV
Sbjct: 241 STPVGSHIMKCAAENIIPSTVELGGKSPNIFFEDIMKAEPSFIEKAAEGLVLAFFNQGEV 300

Query: 301 CTCPSRALIQESIFEPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQ 360
           CTCPSRAL+QESI++ FM+VVM K+  IKRG+PLDTDTMVGAQASEQQFDKILSY+EIA+
Sbjct: 301 CTCPSRALVQESIYDEFMKVVMNKVLQIKRGDPLDTDTMVGAQASEQQFDKILSYLEIAK 360

Query: 361 QEGAQILTGGAAEKLEGSLSTGYYVQPTLIKGHNKMRVFQEEIFGPVVGVATFKDEAEAL 420
            EGA++LTGG  EKLEGSL+TGYY+QPTL+KG NKMRVFQEEIFGPVV + TFKDEAEAL
Sbjct: 361 GEGAELLTGGKVEKLEGSLATGYYIQPTLLKGTNKMRVFQEEIFGPVVSITTFKDEAEAL 420

Query: 421 AIANDTEFGLGAGVWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480
           AIANDTEFGLGAG+WTRDINRAYRMGR IKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET
Sbjct: 421 AIANDTEFGLGAGLWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRET 480

Query: 481 HKMMLDHYQQTKNLLISYDINPLGFF 506
           HKMMLDHYQQTKNLL+SYDINPLGFF
Sbjct: 481 HKMMLDHYQQTKNLLVSYDINPLGFF 506


Lambda     K      H
   0.319    0.136    0.406 

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: 845
Number of extensions: 22
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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: 52 (24.6 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