GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Klebsiella michiganensis M5al

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease

Query= TCDB::P15993
         (457 letters)



>FitnessBrowser__Koxy:BWI76_RS08745
          Length = 459

 Score =  397 bits (1019), Expect = e-115
 Identities = 198/440 (45%), Positives = 287/440 (65%), Gaps = 5/440 (1%)

Query: 5   QQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMR 64
           QQ+   L RGL  RHI+ IALG AIGTGLF GSAS I++AGP ++L Y I G   F++MR
Sbjct: 3   QQNKPHLLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIVMR 62

Query: 65  QLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPE 124
            LGEM V  PV+GSFS +A +Y G  AGF +GW Y    V+VA+A++TA G Y+  WYP+
Sbjct: 63  ALGEMAVRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWYPD 122

Query: 125 IPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLF--SGNGGP 182
           +P W+        I A+NL +V+VFGEMEFW ++IKV+A++AMI+ GG ++F   GN  P
Sbjct: 123 VPRWIWVLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNAFP 182

Query: 183 QATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVI 242
              + NLW  GGF P+G+ G++  + I+MF+FGG+E++G+TAAEA NP++ IP+A N + 
Sbjct: 183 ATGLENLWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINTIP 242

Query: 243 YRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNS 302
            RI++FY+ +LA+L+++ PW       SPFVLIF  LG    A  LNI+V++A++S  NS
Sbjct: 243 LRIVLFYVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAINS 302

Query: 303 CVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLL 362
            ++   RM++G+A++G APK+   +   GVP  T++V  +     V++NYL PE  F L+
Sbjct: 303 DIFGAGRMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQVFVLI 362

Query: 363 MALVVSALVINWAMISLAHMKFRR--AKQEQGVVTRFPALLYPLGNWICLLFMAAVLVIM 420
            +L   A V  W MI LAH   RR  + +E+G +  FP  L+P+   + LLFM  V+ ++
Sbjct: 363 ASLAAFATVWVWVMILLAHFAMRRGLSAEERGNIA-FPVPLWPVAPLLTLLFMGLVIAVL 421

Query: 421 LMTPGMAISVYLIPVWLIVL 440
            M     I++    VWL +L
Sbjct: 422 GMVEETRIALIAGLVWLGLL 441


Lambda     K      H
   0.328    0.141    0.434 

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: 677
Number of extensions: 40
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: 457
Length of database: 459
Length adjustment: 33
Effective length of query: 424
Effective length of database: 426
Effective search space:   180624
Effective search space used:   180624
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: 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