GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Cupriavidus basilensis 4G11

Align High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M (characterized)
to candidate RR42_RS34790 RR42_RS34790 ABC transporter permease

Query= SwissProt::P22729
         (425 letters)



>FitnessBrowser__Cup4G11:RR42_RS34790
          Length = 348

 Score =  161 bits (408), Expect = 3e-44
 Identities = 98/323 (30%), Positives = 169/323 (52%), Gaps = 25/323 (7%)

Query: 86  TVKQKLFLVALLVLAVAWPFMVSRGT-VDIATLTMIYIILGLGLNVVVGLSGLLVLGYGG 144
           T++ K     LL LA+A+P +      + + TL  IY I  LGLN++ G +G L L +GG
Sbjct: 4   TLQGKTGWALLLALAIAFPLVTPNSYYLTVMTLAFIYAIATLGLNLITGYTGQLNLAHGG 63

Query: 145 FYAIGAYTFALLNHYYGLGFWTCLPIAGLMAAAAGFLLGFPVLRLRGDYLAIVTLGFGEI 204
           F AIGAYT  +L   + + FW    ++G++    G+ +G   LRL+G Y +I TL  G I
Sbjct: 64  FMAIGAYTLGILTVDHQVPFWAAFVLSGVVCMMVGYFVGVVSLRLKGHYFSIFTLCIGYI 123

Query: 205 VRILLLNNTEITGGPNGISQIPKPTLFG-LEFSRTAREGGWDTFSNFFGLKYDPSDRVIF 263
           + +L+     +T G  G+  IP P   G L F                       D V  
Sbjct: 124 IYLLIEKWESLTHGTVGLIGIPVPASVGPLAF-----------------------DNVQA 160

Query: 264 LYLVALLLVVLSLFVINRLLRMPLGRAWEALREDEIACRSLGLSPRRIKLTAFTISAAFA 323
            Y + L  +V   F+++R++   LGR++ A+R  +    +LG++  R K+ +F +S  +A
Sbjct: 161 QYYLVLFFLVAGTFLMHRIVTSLLGRSFMAVRNSDALAEALGINLMRTKVLSFVLSVGYA 220

Query: 324 GFAGTLFAARQGFVSPESFTFAESAFVLAIVVLGGMGSQFAVILAAILLVVSRELMRDFN 383
           GFAG L+A +  F+ P+      +  ++  +++GG G+    +L A+L+    + ++   
Sbjct: 221 GFAGALYAGQVRFLGPDIARTDLTFEMVMAMLVGGTGTLLGPLLGAVLVPWVTQTLQFLQ 280

Query: 384 EYSMLMLGGLMVLMMIWRPQGLL 406
           +Y ML+ G ++VL++I+ P G++
Sbjct: 281 DYRMLVFGPVLVLLIIFVPDGIV 303


Lambda     K      H
   0.330    0.145    0.436 

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: 251
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: 425
Length of database: 348
Length adjustment: 30
Effective length of query: 395
Effective length of database: 318
Effective search space:   125610
Effective search space used:   125610
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