GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Pseudovibrio axinellae Ad2

Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate WP_068000560.1 PsAD2_RS00560 ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_21390
         (340 letters)



>NCBI__GCF_001623255.1:WP_068000560.1
          Length = 332

 Score =  193 bits (491), Expect = 5e-54
 Identities = 118/318 (37%), Positives = 183/318 (57%), Gaps = 24/318 (7%)

Query: 26  IFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLS 85
           I L L+ + L F +F          + +  +  ++ QV+I  +LA+G+T VI+  GIDLS
Sbjct: 27  IGLALLALILFFSIF------TEHFLTANNITNILTQVTINLILAVGMTFVILIGGIDLS 80

Query: 86  SGSVLALSAMIAA---SLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIA 142
            GSV+A +++IA    +LA    F   V          + VIA   VG++ GAING+I A
Sbjct: 81  VGSVMAFASVIAGKAITLAGLGPFEAIV----------LAVIAATAVGVVCGAINGTITA 130

Query: 143 VTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHG---AMPVIIFLVVAVIF 199
              +P FI TLGM+  ARG A   +  Q +     ++   G      +PV+  + +A++F
Sbjct: 131 RWSLPSFIITLGMLNIARGAALQASNAQTIYSFPLAFEDFGSAMFYGVPVVFMVALALVF 190

Query: 200 --HIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAAT 257
                L +T +G+  Y IG N +A R +G +V R+ +  ++I GL AG+A VV  AR   
Sbjct: 191 IAWFILNFTVFGRLLYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAAVVYMARLNI 250

Query: 258 GQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDI 317
                G+ +EL+AIAA +IGGTSL GG G + GT+IGA I+GV+A+G   +G+  +++ +
Sbjct: 251 SSPIAGIGFELNAIAAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILIGLSDFMRQM 310

Query: 318 IKGLIIVIAVVIDQYRNK 335
           I G++I+IAV++D YR K
Sbjct: 311 ITGVVIIIAVILDYYRAK 328


Lambda     K      H
   0.326    0.140    0.394 

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: 292
Number of extensions: 14
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: 340
Length of database: 332
Length adjustment: 28
Effective length of query: 312
Effective length of database: 304
Effective search space:    94848
Effective search space used:    94848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 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:

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