GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_5633 Aromatic amino acid transport protein AroP

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Aromatic amino acid
           transport protein AroP
          Length = 472

 Score =  613 bits (1581), Expect = e-180
 Identities = 303/458 (66%), Positives = 358/458 (78%), Gaps = 10/458 (2%)

Query: 2   MEGQQ-HGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAF 60
           M GQ  H  +LKRGLKNRHIQLIALGGAIGTGLFLGSA V++SAGP +ILGYAI GFIAF
Sbjct: 1   MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAF 60

Query: 61  LIMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120
           +IMRQLGEM+VEEPVAGSFSHFA+KYWG FAGF SGWN W+LY+LV M+ELTAVGKYI +
Sbjct: 61  MIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHY 120

Query: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGNG 180
           W P+IPTWVSAA FF++IN INL NVKVFGE EFWFAIIKV+A+V MI  G +LL SG+G
Sbjct: 121 WAPDIPTWVSAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG 180

Query: 181 GPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 240
           GPQA+V+NLW  GGF P+G +GLVM MAIIMFSFGGLE++G TAAEAD P+  IPKA NQ
Sbjct: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240

Query: 241 VIYRILIFYIGSLAVLLSLMPWTRVTA---------DTSPFVLIFHELGDTFVANALNIV 291
           VIYRILIFYIG+L VLLSL PW  + +           SPFV +F  LG    A+ LN V
Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300

Query: 292 VLTAALSVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLIN 351
           VLTAALSVYNS  YCNSRML G+A+QG+APK L+ +DKRGVPV +IL SA VT + VL+N
Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKVLSKIDKRGVPVRSILASAAVTLVAVLLN 360

Query: 352 YLAPESAFGLLMALVVSALVINWAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLL 411
           YL P+ A  LLM+LVV+ LVINWAMIS +H KFR+   +      F AL YP GN+ICL 
Sbjct: 361 YLIPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTHQTPLFKALWYPYGNYICLA 420

Query: 412 FMAAVLVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEK 449
           F+  +L +ML+ PG+ +SVY IPVW++ + + Y  K K
Sbjct: 421 FVVFILGVMLLIPGIQVSVYAIPVWVVFMAVCYWIKNK 458


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: 706
Number of extensions: 30
Number of successful extensions: 2
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: 472
Length adjustment: 33
Effective length of query: 424
Effective length of database: 439
Effective search space:   186136
Effective search space used:   186136
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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