GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter permease (characterized, see rationale)
to candidate AO353_25120 AO353_25120 ABC transporter permease

Query= uniprot:A0A166QFV1
         (320 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25120
          Length = 320

 Score =  615 bits (1586), Expect = 0.0
 Identities = 306/320 (95%), Positives = 316/320 (98%)

Query: 1   MSVSSTHAPCDELLLTRETPVQRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDAN 60
           MSVS+THA CDELLLTRETP+QRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDAN
Sbjct: 1   MSVSTTHASCDELLLTRETPIQRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDAN 60

Query: 61  LADTGGGTFIGFGNYLFHNGSSWSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALL 120
           LADT GG+F+G  NYLFH+GS+WSGILVDPQWWNAVRNTL+FTVVSVGLE+VLGLLVALL
Sbjct: 61  LADTSGGSFVGLSNYLFHDGSNWSGILVDPQWWNAVRNTLHFTVVSVGLEIVLGLLVALL 120

Query: 121 LNIKFTGRALVRALILIPWAIPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTAD 180
           LNIKFTGR+LVRALILIPWAIPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTAD
Sbjct: 121 LNIKFTGRSLVRALILIPWAIPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTAD 180

Query: 181 ADLSMWAVIIVDVWKTVPFVTLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMP 240
           ADLSMWAVIIVDVWKTVPFVTLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMP
Sbjct: 181 ADLSMWAVIIVDVWKTVPFVTLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMP 240

Query: 241 ALLVAAIFRILDSLRVFDVIYVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLV 300
           ALLVAAIFRILDSLRVFDVIYVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLV
Sbjct: 241 ALLVAAIFRILDSLRVFDVIYVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLV 300

Query: 301 VAVIALLYLYLGRRQLEVRS 320
           VAVIA+LYLYLGRRQLEVRS
Sbjct: 301 VAVIAMLYLYLGRRQLEVRS 320


Lambda     K      H
   0.329    0.140    0.443 

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: 442
Number of extensions: 10
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: 320
Length of database: 320
Length adjustment: 28
Effective length of query: 292
Effective length of database: 292
Effective search space:    85264
Effective search space used:    85264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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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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