GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Cupriavidus basilensis 4G11

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS29445 RR42_RS29445 ABC transporter permease

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__Cup4G11:RR42_RS29445
          Length = 358

 Score =  168 bits (426), Expect = 2e-46
 Identities = 101/304 (33%), Positives = 160/304 (52%), Gaps = 34/304 (11%)

Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAAL 201
           +LIY +   GL ++ G  GLL +G+ AF  VGAY+ A L+S+ G+ F   L  +   +AL
Sbjct: 50  VLIYAIAGLGLMVLSGYTGLLSIGHAAFLGVGAYTQAWLTSH-GVPFVPALLAAAALSAL 108

Query: 202 WGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDA 261
            GV++G P LR++G YLAI TLAFG I+  +L  W  VT G  G+  +    L+G   D 
Sbjct: 109 TGVVVGLPALRVKGIYLAIATLAFGLIVEEILARWESVTGGNAGLP-VAAPQLWGYVLDG 167

Query: 262 TAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACR 321
                              +  +YL LA+C+L     + L R   GRA+ A+R+ EI+ +
Sbjct: 168 P------------------VAFYYLSLAVCLLATLAVLNLLRSATGRAFIAIRDSEISAQ 209

Query: 322 SLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSL 381
           S+GI+    K  +FA  A   G AG+ +A +  ++SPE F   +S  +L +VV+GG+GS+
Sbjct: 210 SMGIHLARYKTLSFALSAALVGIAGALYAHKLRYISPEQFGIAQSIDLLLLVVVGGLGSV 269

Query: 382 TGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPEL------YRMLIFGLAMVVVMLFKPR 435
            G  + AI ++   ++        ++   D  P         + L++GL ++  +LF+P 
Sbjct: 270 HGAFLGAIFLIVMPQM--------IVLAKDLLPPAIGQASGMQALVYGLVLMAFVLFEPM 321

Query: 436 GFVG 439
           G  G
Sbjct: 322 GLYG 325


Lambda     K      H
   0.330    0.145    0.432 

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: 482
Number of extensions: 29
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 463
Length of database: 358
Length adjustment: 31
Effective length of query: 432
Effective length of database: 327
Effective search space:   141264
Effective search space used:   141264
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: 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