GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Lutibaculum baratangense AMV1

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_023434295.1 N177_RS20200 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:G8ALI9
         (505 letters)



>NCBI__GCF_000496075.1:WP_023434295.1
          Length = 441

 Score =  493 bits (1270), Expect = e-144
 Identities = 262/482 (54%), Positives = 328/482 (68%), Gaps = 50/482 (10%)

Query: 4   ISMSSPRAIAWPSILKEAAMTAFVALLLTIPLVGLRTVDRPTGLGLETRWNEVAAAVGLV 63
           ++ +SP       ++K+AA +A +AL L  P++GL+TV    GLGL  RW++V       
Sbjct: 1   MATTSPSRRPAAELVKDAAYSALIALALAAPIIGLQTVTARGGLGLNARWDDV------- 53

Query: 64  FLGRLGLCLIREGHAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGAVIAIRAVLAIRT 123
                                        F I +   A R++L            +    
Sbjct: 54  -----------------------------FLIVLAVFAGRLLL---------NFTIWRHQ 75

Query: 124 GRSKLSQAERDKRMDHIAAQVQHA-SRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTY 182
           G   + Q    +      A+  H  S+ +GP+A+ VAL  P  P +DR ++D+ I++LTY
Sbjct: 76  GARPIGQKWFQRAGGRPFARHGHTLSKIIGPLALAVALLLPALPFSDRYVMDLSIMVLTY 135

Query: 183 IMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVL 242
           IMLGWGLNIVVGLAGLLDLGYVAFYA+GAYS+ALLA +F   FW+CLPLAG LAA  GV+
Sbjct: 136 IMLGWGLNIVVGLAGLLDLGYVAFYAIGAYSFALLATHFDLGFWICLPLAGILAAFWGVI 195

Query: 243 LGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPA 302
           LGFPVLRLRGDY AIVTL FGEIIR++L+NWY+FTGGPNGI GIP P+ FG+ +F R   
Sbjct: 196 LGFPVLRLRGDYLAIVTLAFGEIIRVVLLNWYEFTGGPNGILGIPDPTLFGL-EFAR--- 251

Query: 303 EGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIAC 362
            G   FHE FGL +S +H+IIFLYY+IL LAL+ N  T+R+R+LP+GRAWEALRED+IAC
Sbjct: 252 RGDNTFHEFFGLSYSSMHKIIFLYYIILCLALITNFVTLRLRRLPVGRAWEALREDEIAC 311

Query: 363 ASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGS 422
            SLGIN TN KL AFAI AMFGGFAGSFFATRQGFISPESFTFIESA+ILAIVVLGG+GS
Sbjct: 312 RSLGINTTNTKLTAFAIGAMFGGFAGSFFATRQGFISPESFTFIESALILAIVVLGGLGS 371

Query: 423 QIGVVVAAFLVIGLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKG 482
           Q+GVV+AA +++G  E FRE   YRML FG+ MV IM+WRPRGL++ R P+++L  R   
Sbjct: 372 QVGVVIAAIVMMGGFEYFREFEQYRMLIFGLAMVFIMVWRPRGLISTRSPSVILKERKAI 431

Query: 483 GA 484
           GA
Sbjct: 432 GA 433


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: 685
Number of extensions: 42
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 505
Length of database: 441
Length adjustment: 33
Effective length of query: 472
Effective length of database: 408
Effective search space:   192576
Effective search space used:   192576
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