GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Pseudomonas litoralis 2SM5

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_090272109.1 BLU11_RS03760 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:G8ALI9
         (505 letters)



>NCBI__GCF_900105005.1:WP_090272109.1
          Length = 418

 Score =  395 bits (1014), Expect = e-114
 Identities = 198/317 (62%), Positives = 243/317 (76%), Gaps = 3/317 (0%)

Query: 156 VVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYA 215
           +  AL +PF    +R  +D+  L+L Y+MLG GLNIVVGLAGLLDLGYV FYAVGAY+YA
Sbjct: 99  IAAALVWPF--FGNRSNIDMATLVLIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYA 156

Query: 216 LLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQ 275
           LLA YFG  FW  L  AG +AA+ G LLGFPVLRLRGDY AIVTLGFGEIIRI+L N   
Sbjct: 157 LLAMYFGIGFWTGLVAAGAMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLNNLTS 216

Query: 276 FTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALV 335
            T GPNGI  IP+P  FG+ +F+R  +EG   FH+ FG+EF+ +HR++FLY+L L+L L+
Sbjct: 217 LTNGPNGIGSIPKPELFGL-EFSRRASEGMQTFHDFFGIEFNSVHRVMFLYFLALLLVLL 275

Query: 336 VNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQ 395
                 R+ ++P+GRAWEA+RED++AC SLGIN T +KL AF I A F GFAG FFA RQ
Sbjct: 276 TLFVINRLLRMPVGRAWEAMREDEVACRSLGINPTAVKLNAFTIGATFAGFAGCFFAARQ 335

Query: 396 GFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFGMGM 455
           GFISPESFTFIESAIILAIVVLGGMGSQ+GV++AA ++  LPE  R+  +YRML FG+ M
Sbjct: 336 GFISPESFTFIESAIILAIVVLGGMGSQLGVILAAIIMTLLPEVARQFDEYRMLLFGLLM 395

Query: 456 VLIMLWRPRGLLAHRDP 472
           VL+M+WRP+GLL  + P
Sbjct: 396 VLMMIWRPQGLLPMKRP 412


Lambda     K      H
   0.329    0.144    0.438 

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: 620
Number of extensions: 38
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 505
Length of database: 418
Length adjustment: 33
Effective length of query: 472
Effective length of database: 385
Effective search space:   181720
Effective search space used:   181720
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: 51 (24.3 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