GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proY in Cupriavidus basilensis 4G11

Align Proline-specific permease (ProY) (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter

Query= TCDB::P37460
         (456 letters)



>FitnessBrowser__Cup4G11:RR42_RS33495
          Length = 465

 Score =  393 bits (1009), Expect = e-114
 Identities = 206/447 (46%), Positives = 285/447 (63%), Gaps = 7/447 (1%)

Query: 7   LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66
           LKRGL  RHI+ +ALG AIGTGLF G A  IKMAGPSVLL Y + G+ A+ IMR LGEM 
Sbjct: 13  LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72

Query: 67  VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126
           V  P A SFS +A +  G  AG+++GW Y    ++V++A+++A GIY+  W+P +P W  
Sbjct: 73  VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132

Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186
            L   L+I AINL SVK FGE+EFWFS  KV  I+ MIV G  ++    G  G    + N
Sbjct: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLA--SGTAGPQASVSN 190

Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246
           LW +GGFF NG  G++M++ ++MF++GG+E++GITA EA +PEK+IP+A N V  RIL+F
Sbjct: 191 LWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIF 250

Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306
           YVG L V++S+YPW +V T GSPFVL F  M     A++LN VVLTA+LS  NS V+   
Sbjct: 251 YVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCNS 310

Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLATF 366
           RML G+A+QG+APK   K ++RGIP   + V  +A    V +NY MP   F ++  L   
Sbjct: 311 RMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLVVS 370

Query: 367 ATVWVWIMILLSQIAFRR--RLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPD 424
           A +  W MI +  + FRR  R   +E    +FK  G  +T    L FL  I+ ++   P 
Sbjct: 371 ALIINWAMISIIHLKFRRDKRAAGQET---RFKSLGYPLTNYVCLAFLAGILYVMYLTPG 427

Query: 425 TRISLYVGFAWIVLLLIGWIFKRRRDR 451
            RIS+Y+  AW+ +L + +  ++++ R
Sbjct: 428 LRISVYLIPAWLAVLGLSYRLRQKQKR 454


Lambda     K      H
   0.329    0.143    0.449 

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: 584
Number of extensions: 30
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: 456
Length of database: 465
Length adjustment: 33
Effective length of query: 423
Effective length of database: 432
Effective search space:   182736
Effective search space used:   182736
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: 51 (24.3 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