GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Escherichia coli BW25113

Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate 14258 b0112 aromatic amino acid transporter (NCBI)

Query= SwissProt::P41815
         (604 letters)



>FitnessBrowser__Keio:14258
          Length = 457

 Score =  196 bits (497), Expect = 2e-54
 Identities = 120/405 (29%), Positives = 204/405 (50%), Gaps = 15/405 (3%)

Query: 78  KSMKSNNHLKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGYVMVSFVTYF 137
           +  +    LK+ +K+RH+ +++LG  IGTGL + +A  +  AGPG +++GY +  F+ + 
Sbjct: 3   EGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPG-IILGYAIAGFIAFL 61

Query: 138 MVQAAGEMGVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLELITSSMTVKY 197
           +++  GEM V  P + G+F+ +   +     GFA+ W + + ++ V   EL      +++
Sbjct: 62  IMRQLGEMVVEEP-VAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120

Query: 198 WNDTINADVFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILSVVINCGGAG 257
           W   I   V   +F+V +  I+   VK +GE EF F   K++ V   II    +   G G
Sbjct: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG 180

Query: 258 VDGYIGGKYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSINEQSNPRKSTP 317
                    W   G    G     F G+  ++    FSFGG+EL  ++  E  NP +S P
Sbjct: 181 GPQATVSNLWDQGGFLPHG-----FTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIP 235

Query: 318 VAAKRSVYRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAASIHKVRVIPHI 377
            A  + +YRILI Y+ ++ ++   +P                SP+VL         + + 
Sbjct: 236 KATNQVIYRILIFYIGSLAVLLSLMPWTR--------VTADTSPFVLIFHELGDTFVANA 287

Query: 378 INAVILISVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRALVVCSLVGVVG 437
           +N V+L + +SV NS +Y   R++  LAQQG APK L  +D+ G P+  ++V +LV  + 
Sbjct: 288 LNIVVLTAALSVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALC 347

Query: 438 FVACSPQEEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQG 482
            +      E AF  L A+   + +  W+ I L+H++FR+A + QG
Sbjct: 348 VLINYLAPESAFGLLMALVVSALVINWAMISLAHMKFRRAKQEQG 392


Lambda     K      H
   0.324    0.138    0.420 

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: 608
Number of extensions: 23
Number of successful extensions: 6
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: 604
Length of database: 457
Length adjustment: 35
Effective length of query: 569
Effective length of database: 422
Effective search space:   240118
Effective search space used:   240118
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