GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08240 in Herbaspirillum seropedicae SmR1

Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate HSERO_RS08280 HSERO_RS08280 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:G8ALI9
         (505 letters)



>FitnessBrowser__HerbieS:HSERO_RS08280
          Length = 408

 Score =  397 bits (1020), Expect = e-115
 Identities = 207/402 (51%), Positives = 270/402 (67%), Gaps = 4/402 (0%)

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

Query: 135 KRMDHIAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVG 194
            ++  +        R    I ++ AL +PF     R  +D+  L L Y++LG GLNIVVG
Sbjct: 67  IKLPALPRMQPRQQRAAVMILLMAALVWPF--FGSRGYVDVMTLALIYVVLGLGLNIVVG 124

Query: 195 LAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDY 254
            AGLLDLGYV FYAVGAY+YAL   YFG +FW C+PLA   +A+ G LLGFPVLRLRGDY
Sbjct: 125 FAGLLDLGYVGFYAVGAYTYALCNQYFGLTFWECVPLAAAASALFGFLLGFPVLRLRGDY 184

Query: 255 FAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGL 314
            AIVTLGFGEIIR++L N    TGGP+G+SGIP+P+ FG+        EG   FH++FGL
Sbjct: 185 LAIVTLGFGEIIRLLLNNMTSITGGPDGVSGIPKPTVFGLVMARNPVTEGGTTFHQLFGL 244

Query: 315 EFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKL 374
            +   H +IFLY+L L++ L     T R+ ++P+GRAWEALRED+IAC SLGIN T +KL
Sbjct: 245 SYQGGHMVIFLYFLALLMVLFTYFVTSRLLRMPMGRAWEALREDEIACRSLGINPTKVKL 304

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

Query: 435 GLPEAFRELADYRMLAFGMGMVLIMLWRPRGLLAHRDPTILL 476
            LPE  R  A+YRML FG+ MVL+M+WRP+GLL    P + L
Sbjct: 365 VLPELARSFAEYRMLIFGLVMVLMMMWRPQGLLPATRPHVEL 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: 601
Number of extensions: 32
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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