GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Marinobacter adhaerens HP15

Align ABC transporter permease (characterized, see rationale)
to candidate GFF3113 HP15_3056 high-affinity branched-chain amino acid ABC transporter, permease protein

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Marino:GFF3113
          Length = 307

 Score =  240 bits (613), Expect = 3e-68
 Identities = 132/303 (43%), Positives = 197/303 (65%), Gaps = 15/303 (4%)

Query: 6   QQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCI-GMMQGAMPGA 64
           QQ+INGL +GS YALIA+GYTMVYGII +INFAHGE+ MIGA T+   I G+    +   
Sbjct: 9   QQLINGLTIGSTYALIAIGYTMVYGIIGMINFAHGEIYMIGAYTALIAITGLAALGIAWL 68

Query: 65  PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124
           P  +IL++A + A +V++++ + +E+VAYRP+R   RL PLI+AIGMSI LQ    +   
Sbjct: 69  P--LILIVALLCAMIVSSSMGWAVERVAYRPVRGRHRLIPLISAIGMSIFLQNYVHLAQG 126

Query: 125 PNYKPYPTMLPSS-PFEIGGAF---ITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180
                +P ++     F  G  F   ++  QI I   T + + +L   ++ +  GRA RA 
Sbjct: 127 SRNIGFPALIDGGFNFGSGDGFQMSLSYMQITIFITTLICMTALSLFISRSRTGRACRAV 186

Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240
           +++  +A+L+G+  + +ISATF+IGA LAA+AG++    YG+     GF+ GLKAFTAAV
Sbjct: 187 SQDLGMANLLGIDTNRIISATFVIGAALAAVAGLLLGMYYGSVDPLFGFIAGLKAFTAAV 246

Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
            GGIG++ GA++GG++LG+ E++ SGY        L   Y D+ +F +LI+IL  +P+GL
Sbjct: 247 LGGIGSIPGAMLGGLILGVAESMTSGY--------LSGEYKDVISFSLLILILLFKPTGL 298

Query: 301 LGE 303
           LG+
Sbjct: 299 LGK 301


Lambda     K      H
   0.327    0.142    0.419 

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: 263
Number of extensions: 10
Number of successful extensions: 4
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: 309
Length of database: 307
Length adjustment: 27
Effective length of query: 282
Effective length of database: 280
Effective search space:    78960
Effective search space used:    78960
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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