Alignments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens FW300-N2E3

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate AO353_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21385
          Length = 521

 Score =  400 bits (1027), Expect = e-116
 Identities = 208/490 (42%), Positives = 315/490 (64%), Gaps = 4/490 (0%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L   N+ K FPGV AL  V   V  G V  LMGENGAGKSTL+KI+ G YQPD+G + + 
Sbjct: 28  LEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLR 87

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKRFVRE 123
           G  V F +  +++ AGIA+IHQEL  +P +++AEN+ +G +  N    ++ RE  R   +
Sbjct: 88  GKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQ 147

Query: 124 RLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLV 183
            LE + + LDP  ++  LSIA+RQMVEI KA+  ++ ++ +DEPTS+++ +E   LF ++
Sbjct: 148 LLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSII 207

Query: 184 RDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREIS 243
            DL+A  + +IYI+H+M+E++ + D   +FRDG  I      + +  D+++S MVGRE+S
Sbjct: 208 ADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQ-RADSMDGDSLISMMVGRELS 266

Query: 244 DIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGAD 303
            ++    +P+G++  + + +    + +  SF++  GEI+G  GL+G+GR+ +   ++G  
Sbjct: 267 QLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 326

Query: 304 HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRV 363
              GGE+ LDG+P+++     AI  G  L  EDRK  G+    +V EN+ ++   HY   
Sbjct: 327 PSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGN 386

Query: 364 GMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDE 423
           G F+ +K      +   K L++KTPS  Q I  LSGGNQQKA+L+RWL   + +++ILDE
Sbjct: 387 G-FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM-TNPRILILDE 444

Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483
           PTRGIDVGAK EIY +I  LA  G A++MISSELPEVLG+SDR++VM +G + G L R +
Sbjct: 445 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 504

Query: 484 ATEQSVLSLA 493
           AT++ V+ LA
Sbjct: 505 ATQERVMQLA 514



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 64/248 (25%), Positives = 119/248 (47%), Gaps = 9/248 (3%)

Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314
           E+   +KG  G          VR G ++   G  GAG+S LM ++ G      GEL L G
Sbjct: 29  EIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRG 88

Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374
           KP+   +   A++ GI +     +E  ++   +++ENI I   R  L     +D ++   
Sbjct: 89  KPVTFDTPLAALQAGIAMI---HQELNLMPHMSIAENIWIG--REQLNGFHMIDHREMHR 143

Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKH 434
              + ++ L+I      Q +  LS   +Q   +++ ++  D  ++I+DEPT  I      
Sbjct: 144 CTAQLLERLRINLDPEEQ-VGNLSIAERQMVEIAKAVSY-DSDILIMDEPTSAITDKEVA 201

Query: 435 EIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATE-QSVLSLA 493
            ++++I  L  +G  I+ I+ ++ EV  ++D + V R G   G L R D+ +  S++S+ 
Sbjct: 202 HLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIG-LQRADSMDGDSLISMM 260

Query: 494 LPQSSTAL 501
           + +  + L
Sbjct: 261 VGRELSQL 268


Lambda     K      H
   0.320    0.136    0.385 

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: 627
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 521
Length adjustment: 35
Effective length of query: 477
Effective length of database: 486
Effective search space:   231822
Effective search space used:   231822
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
the source code
instructions for running GapMind on your computer

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