GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Pseudomonas litoralis 2SM5

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_090272109.1 BLU11_RS03760 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:A0A165KER0
         (358 letters)



>NCBI__GCF_900105005.1:WP_090272109.1
          Length = 418

 Score =  272 bits (696), Expect = 1e-77
 Identities = 164/354 (46%), Positives = 218/354 (61%), Gaps = 49/354 (13%)

Query: 5   KTNWIIGAVALLVLPLILQSFGN-AWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAF 63
           +  W     A LV P     FGN + + +A L L+YV+L LGLNIVVG AGLLDLGYV F
Sbjct: 92  RLTWCFLIAAALVWPF----FGNRSNIDMATLVLIYVMLGLGLNIVVGLAGLLDLGYVGF 147

Query: 64  YAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123
           YAVGAY +AL+A              F  G     W  +  A  +AA FG +LG P L+L
Sbjct: 148 YAVGAYTYALLAM------------YFGIGF----WTGLVAAGAMAALFGFLLGFPVLRL 191

Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL------- 176
           RGDYLAIVTLGFGEIIRI LNNL    +LTNGP G+G I   ++FGL+  +R        
Sbjct: 192 RGDYLAIVTLGFGEIIRILLNNL---TSLTNGPNGIGSIPKPELFGLEFSRRASEGMQTF 248

Query: 177 -EVFGFDINSV---TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGIN 232
            + FG + NSV      Y+L L+LV++++ +  RL    +GRAW A+REDE+A +++GIN
Sbjct: 249 HDFFGIEFNSVHRVMFLYFLALLLVLLTLFVINRLLRMPVGRAWEAMREDEVACRSLGIN 308

Query: 233 TRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVIL 292
              +KL AF +GA+F G +G  F A QGF+SPESF+ +ES +I+A+VVLGG+G   GVIL
Sbjct: 309 PTAVKLNAFTIGATFAGFAGCFFAARQGFISPESFTFIESAIILAIVVLGGMGSQLGVIL 368

Query: 293 GAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
            A++++ LPEV R            + D    R LL  L M+++M+ RP+GL P
Sbjct: 369 AAIIMTLLPEVAR------------QFDE--YRMLLFGLLMVLMMIWRPQGLLP 408


Lambda     K      H
   0.328    0.144    0.430 

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: 376
Number of extensions: 14
Number of successful extensions: 5
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: 358
Length of database: 418
Length adjustment: 30
Effective length of query: 328
Effective length of database: 388
Effective search space:   127264
Effective search space used:   127264
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 (21.7 bits)
S2: 50 (23.9 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