GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate AO353_16275 AO353_16275 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_16275
          Length = 244

 Score =  285 bits (730), Expect = 5e-82
 Identities = 143/242 (59%), Positives = 178/242 (73%), Gaps = 2/242 (0%)

Query: 14  IIQMQGVNKWYGQFHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIVV 73
           +I ++ VNKWYG F VL D +  VK+GE IV+CGPSGSGKST I+C+N LE  Q+G +VV
Sbjct: 1   MISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVVV 60

Query: 74  DGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMHY 133
           DG  + +    +  +R  VGMVFQHF LFPHLTI +N T+A + V    K +A +  +  
Sbjct: 61  DGTSIADPKTDLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120

Query: 134 LERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTMI 193
           LERV +   AHK+PGQLSGGQQQRVAIARAL M P +MLFDEPTSALDPEMV EVLD M+
Sbjct: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180

Query: 194 GLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFD--NPQNDRTKLFLSQ 251
            LA +GMTM+CVTHEMGFAR VA+RVIFMD+G+I+E     +FF   N ++DR + FL +
Sbjct: 181 QLANEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARSDRAQHFLDK 240

Query: 252 IL 253
           IL
Sbjct: 241 IL 242


Lambda     K      H
   0.322    0.137    0.407 

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: 210
Number of extensions: 4
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: 254
Length of database: 244
Length adjustment: 24
Effective length of query: 230
Effective length of database: 220
Effective search space:    50600
Effective search space used:    50600
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 (21.9 bits)
S2: 46 (22.3 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