GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Cupriavidus basilensis 4G11

Align arginine permease (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease

Query= CharProtDB::CH_091699
         (590 letters)



>FitnessBrowser__Cup4G11:RR42_RS33780
          Length = 474

 Score =  253 bits (646), Expect = 1e-71
 Identities = 158/442 (35%), Positives = 227/442 (51%), Gaps = 26/442 (5%)

Query: 80  QNAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQS 139
           Q++ +K  LKQRH+ MIALGG IG GLF+G    + +AGP  A+IS+L  G L   V + 
Sbjct: 9   QSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPA-AVISFLITGLLVVLVMRM 67

Query: 140 LGEMATFIPVTSSFTVFSQRFLS--PAFGAA----NGYMYWFSWAITFALELSVVGQVIQ 193
           LGEMA  +P   SF  +++   S  PA G       G+MYW+ W I  ALE      ++Q
Sbjct: 68  LGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGASLVQ 127

Query: 194 FWTYKVPLAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIYCFCMVCGAG 253
           FW   VP  +   +  V++T+ NL  VK +GEFEFW ASIKV AI+ FL      V G  
Sbjct: 128 FWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAGLFVLGMW 187

Query: 254 VTGPVGFRYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANP 313
                   +    G + P  I         +  ++  + A   + G E+V I A E A P
Sbjct: 188 PGATASVAHLTVHGGFAPNGI---------MPVLTGAVAATGFYFGAEIVTIAAAETAEP 238

Query: 314 RKSVPRAIKKVVFRILTFYIGSLLFIGLLVPYNDPKLTQSTSYVSTSPFIIAIENSGTKV 373
           +K+V RA   V+ R+L FY+GS+L +  LVP+N   +         +P++ A+       
Sbjct: 239 QKAVARATSSVITRVLVFYVGSVLLVVCLVPWNSAGIA--------TPYVSALNAMRIPA 290

Query: 374 LPHIFNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAF 433
              I NAV+LT ++SA NS +Y  SR+LF L+K   APK L+R ++ GVP  A+     F
Sbjct: 291 AAQIMNAVVLTAVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLF 350

Query: 434 GALAYMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELPFKAK 493
           G  A + +    DKVF +L+N  G    F ++ I+IS +R    L+     R  L  +  
Sbjct: 351 GYGAVVMSYVSPDKVFAFLVNSYGTVAIFVYILIAISQLRLRARLEREAPHR--LKVRMW 408

Query: 494 LMPGLAYYAATFMTIIIIIQGF 515
             P L + A   M  I++   F
Sbjct: 409 AFPYLTWVAIAGMVGIVVAMAF 430


Lambda     K      H
   0.325    0.140    0.438 

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: 686
Number of extensions: 44
Number of successful extensions: 5
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: 590
Length of database: 474
Length adjustment: 35
Effective length of query: 555
Effective length of database: 439
Effective search space:   243645
Effective search space used:   243645
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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