GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00890 in Burkholderia phytofirmans PsJN

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein

Query= uniprot:D8IUY5
         (404 letters)



>FitnessBrowser__BFirm:BPHYT_RS31745
          Length = 389

 Score =  430 bits (1105), Expect = e-125
 Identities = 222/372 (59%), Positives = 270/372 (72%), Gaps = 22/372 (5%)

Query: 17  ISLLLLLALMIVFPFVAQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLDLGYIAFYA 76
           IS L  + +  +   +    GN  VR++D A+LY+MLALGLN+VVGFAGLLDLGYIAFYA
Sbjct: 25  ISALTAIGVTALPLLIGAAAGNYGVRVLDFAMLYVMLALGLNIVVGFAGLLDLGYIAFYA 84

Query: 77  IGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWLIVPISAFLA 136
           +GAY+A LL SP  AA  E   + +PS                G H   W ++P++  LA
Sbjct: 85  VGAYTAALLTSPHLAAHFEWIGHMWPS----------------GFHAPYWFVMPVAMVLA 128

Query: 137 ALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPIKVFG 196
           A+ G  LGAPTL+LRGDYLAIVTLGFGEI+RIFMNNL+ PVNITNGPQGI  + P+ V G
Sbjct: 129 AIAGICLGAPTLRLRGDYLAIVTLGFGEIVRIFMNNLDRPVNITNGPQGITGVAPVTVAG 188

Query: 197 VSLAGEPGSGSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQDSRLGRAWVAIREDE 256
            +L+            G    +V  YY++F+L  + V++   RLQ SR+GRAW AIREDE
Sbjct: 189 FNLSETHA------FLGFQFTTVYMYYYVFVLCSLLVVWVCTRLQHSRIGRAWAAIREDE 242

Query: 257 IAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIAVLAMVVLGG 316
           IAAKAMGINTRNVKLLAFAMGASFGG++GAMF  FQGFVSPESF+L ES+ VLA VVLGG
Sbjct: 243 IAAKAMGINTRNVKLLAFAMGASFGGLSGAMFAGFQGFVSPESFTLWESVTVLACVVLGG 302

Query: 317 IGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGLAMVVIMLTRP 376
           +GHIPGV+ G V+LA LPE+LR  + P+Q AIFG V +D EV+RQLLYGLAMV+IML RP
Sbjct: 303 MGHIPGVIFGAVLLAILPEILRSTMTPLQNAIFGHVIVDTEVIRQLLYGLAMVIIMLRRP 362

Query: 377 AGLWPSPRHEDR 388
            GLWP+P+HEDR
Sbjct: 363 EGLWPAPKHEDR 374


Lambda     K      H
   0.327    0.143    0.430 

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: 494
Number of extensions: 10
Number of successful extensions: 3
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: 404
Length of database: 389
Length adjustment: 31
Effective length of query: 373
Effective length of database: 358
Effective search space:   133534
Effective search space used:   133534
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: 50 (23.9 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