GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS31745 BPHYT_RS31745 ABC
           transporter ATP-binding protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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