Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3559 Aromatic amino acid transport protein AroP

Query= TCDB::P15993
         (457 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559
          Length = 473

 Score =  611 bits (1575), Expect = e-179
 Identities = 305/458 (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 FFV+IN INL NVKVFGE EFWFAIIKV+A+V MI  G +LL SG+G
Sbjct: 121 WAPDIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGDG 180

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

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

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

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

Query: 412 FMAAVLVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEK 449
           F+  +L +ML+ PG+ ISVY IPVW+  + + Y  K K
Sbjct: 421 FVVFILGVMLLIPGIQISVYAIPVWVAFMWVCYGIKNK 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: 702
Number of extensions: 28
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: 473
Length adjustment: 33
Effective length of query: 424
Effective length of database: 440
Effective search space:   186560
Effective search space used:   186560
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources