GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Herbaspirillum autotrophicum IAM 14942

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:G8ALI9
         (505 letters)



>NCBI__GCF_001189915.1:WP_050462656.1
          Length = 408

 Score =  400 bits (1028), Expect = e-116
 Identities = 213/402 (52%), Positives = 271/402 (67%), Gaps = 4/402 (0%)

Query: 77  HAVTVLVLAAAATAAGFFIAMPTEALRVILIAGGA--VIAIRAVLAIRTGRSKLSQAERD 134
           +AV   +L A  T     + +  E  RV+L A     +IA+ AV   +  +  LS+   +
Sbjct: 7   NAVAAAILTAILTTPLLGLKLQLEGYRVVLQAHWTPVLIAVLAVFLFQLFKPALSRTTAN 66

Query: 135 KRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVG 194
            R+  +        R+   + + VAL +PF     R  +D+  L L Y++LG GLNIVVG
Sbjct: 67  IRLPALPKLQPTQQRYALMVLLAVALVWPF--FGSRGNVDVVTLALIYVVLGLGLNIVVG 124

Query: 195 LAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDY 254
            AGLLDLGYV FYAVG Y+YALL  YFG SFW CLPLA  ++A+ G LLGFPVLRLRGDY
Sbjct: 125 FAGLLDLGYVGFYAVGGYTYALLNQYFGLSFWECLPLAAGMSALFGFLLGFPVLRLRGDY 184

Query: 255 FAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGL 314
            AIVTLGFGEIIR++L N    TGGP+G+SGIP+P+ FGI        EG   FH+M GL
Sbjct: 185 LAIVTLGFGEIIRLLLNNLTSLTGGPDGVSGIPKPTVFGIEMARTASVEGGTTFHDMLGL 244

Query: 315 EFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKL 374
            +   H +IFLY+L L+L L     T R+ ++P+GRAWEALR+D+IAC SLGIN T +KL
Sbjct: 245 TYQGGHMVIFLYFLGLLLVLFTYFVTSRLIRMPMGRAWEALRDDEIACRSLGINPTKIKL 304

Query: 375 AAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVI 434
           +AF + A F G AGSFFA RQG ++PESFTFIESA+ILAIVVLGGMGSQ+GV++AA L+ 
Sbjct: 305 SAFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLGGMGSQLGVILAAILLT 364

Query: 435 GLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476
            LPE  R  A+YRML FG+ MVL+M+WRP+GLL    P + L
Sbjct: 365 ILPEVARSFAEYRMLIFGLVMVLMMIWRPQGLLPATRPHVEL 406


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: 632
Number of extensions: 34
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: 408
Length adjustment: 33
Effective length of query: 472
Effective length of database: 375
Effective search space:   177000
Effective search space used:   177000
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 Apr 09 2024. 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