GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Paraburkholderia bryophila 376MFSha3.1

Align Fructose import permease protein FrcC (characterized)
to candidate H281DRAFT_03225 H281DRAFT_03225 mannose ABC transporter membrane protein /fructose ABC transporter membrane protein /ribose ABC transporter membrane protein

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__Burk376:H281DRAFT_03225
          Length = 328

 Score =  265 bits (678), Expect = 1e-75
 Identities = 141/317 (44%), Positives = 199/317 (62%), Gaps = 9/317 (2%)

Query: 40  QHFLHSSPAAV---PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLV 96
           +HF    P+     PLI LVL+   F +    +F S   ++LILQQ  +V ++   QTL+
Sbjct: 12  RHFSDRLPSLAEVGPLIALVLAC-GFFISQSSRFLSFQNLSLILQQTMVVAVIAIGQTLI 70

Query: 97  ILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLP 156
           +LT GIDLS G +M   S+IM +F    G PPAL+++CG+G   L G +NG L+ R+KLP
Sbjct: 71  VLTGGIDLSCGMVMAFGSIIMTKFAVTLGLPPALAILCGIGASTLFGVLNGVLITRIKLP 130

Query: 157 PFIVTLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVL 216
            FIVTLG   I  A   +YS      A+ +S     + FFG  F++G A  TYG V+ +L
Sbjct: 131 AFIVTLGTLNIAFALTQIYS-----NAESVSNLPDAIMFFGNTFKLGPADVTYGTVLTLL 185

Query: 217 LVCLLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGR 276
           +    W+VL  T  GR++YA+G++ EAA+L G++  ++L+++YTL+G I  +A    + R
Sbjct: 186 MYLATWFVLRDTVPGRHLYALGNNAEAARLMGLSSQKILLTVYTLAGAIYGVAALLSVSR 245

Query: 277 IGSVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQW 336
            G   P AGQ  N++SITAVV+GG SLFGGRGSI G L GALIVGVF  GL L+G    +
Sbjct: 246 TGVGDPQAGQTENLDSITAVVLGGTSLFGGRGSISGTLLGALIVGVFRNGLTLIGVSSVY 305

Query: 337 TYLLIGLLIIIAVAIDQ 353
             L+ G+L+I+AVA D+
Sbjct: 306 QVLITGMLVILAVAADK 322


Lambda     K      H
   0.327    0.141    0.420 

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: 362
Number of extensions: 20
Number of successful extensions: 2
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: 360
Length of database: 328
Length adjustment: 29
Effective length of query: 331
Effective length of database: 299
Effective search space:    98969
Effective search space used:    98969
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: 49 (23.5 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