Alignments for a candidate for ytfR in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Pseudomonas fluorescens GW456-L13

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  312 bits (799), Expect = 2e-89
 Identities = 186/470 (39%), Positives = 268/470 (57%), Gaps = 7/470 (1%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   G+ K +     L  +D +L RGE++AL GENGAGKSTL K + G+     G +  
Sbjct: 9   VLSVSGIGKTY-AQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQY 67

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +GQ   P + A A+ LGI  V QE+NLLP +SVA+NLF+   P + G + RK++ K A E
Sbjct: 68  QGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAIE 127

Query: 129 LMASYGF-SLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
            MA  G  ++D    +    +  QQ+V I R +     VLILDEPTA L  +EVE+LF+ 
Sbjct: 128 AMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
           + +L+ RGVS+I+++H L+++ +V+ RI VLR+G+ V           +LV +M+GREL 
Sbjct: 188 ITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELG 247

Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
            H    A +      PV       +   +     EVR GEI G++GL+G+GRTE   +IF
Sbjct: 248 EHIDMGARKI---GAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIF 304

Query: 308 GIKPADSGTALIKGKPQ--NLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
           G   ADSGT  +    Q  N+RSP  A   GI    EDRK +G++   S+  NI L    
Sbjct: 305 GADIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGNMP 364

Query: 366 QRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLI 425
                  +   +++ +A+R I  + IR+    Q +  LSGGNQQKV++ RWL      L+
Sbjct: 365 GISGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLL 424

Query: 426 LDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475
            DEPTRGIDVGA  +I  L+  L   G AL+V+SS+L EL+   DR+ ++
Sbjct: 425 FDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVL 474



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 63/213 (29%), Positives = 107/213 (50%), Gaps = 7/213 (3%)

Query: 276 IAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVL 335
           +A  DL +  GE++ L G  G+G++  +++I G+    +G    +G+     S  QA  L
Sbjct: 24  LAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDYRPGSRAQAEAL 83

Query: 336 GIGFCPEDRKTDGIIAAASVRENIILA-LQAQRGWLRPISRKEQQEIAERFIRQLGIRTP 394
           GI    ++     ++   SV EN+ L  L ++ GW   ISRK+ ++ A   +  +G+   
Sbjct: 84  GIRMVMQELN---LLPTLSVAENLFLDNLPSKGGW---ISRKQLRKAAIEAMAHVGLDAI 137

Query: 395 STEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLA 454
             +  +  L  G+QQ V ++R L+     LILDEPT  +       +   I  L + G++
Sbjct: 138 DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVS 197

Query: 455 LLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487
           ++ IS  LEEL   A R+ ++RD   V   P+A
Sbjct: 198 IIYISHRLEELARVAQRIAVLRDGNLVCVEPMA 230



 Score = 76.3 bits (186), Expect = 2e-18
 Identities = 71/260 (27%), Positives = 120/260 (46%), Gaps = 14/260 (5%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   GLS+       + +V F +R GEI  + G  GAG++ L++ + G   AD GTI L
Sbjct: 261 VLTVNGLSRS----DKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIAL 316

Query: 69  --EGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPKRFG---LLRRK 120
               Q I+ ++   A   GI  + ++     LL   S+  N+ +G  P   G   +   K
Sbjct: 317 GAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGNMPGISGAGFVDNDK 376

Query: 121 EMEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQE 180
           E      ++ A    S    + ++  S   QQ V I R ++    VL+ DEPT  +D   
Sbjct: 377 ERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDEPTRGIDVGA 436

Query: 181 VELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKM 240
              +++L+ +L  +G +L+ V+  L ++  + DRI VL  GS +   +     Q EL+  
Sbjct: 437 KFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDSWTQDELLAA 496

Query: 241 MLG--RELDTHALQRAGRTL 258
                ++ D   ++ A R L
Sbjct: 497 AFAGYQKRDAQLVEAAPRDL 516


Lambda     K      H
   0.321    0.138    0.391 

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: 575
Number of extensions: 27
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 500
Length of database: 517
Length adjustment: 34
Effective length of query: 466
Effective length of database: 483
Effective search space:   225078
Effective search space used:   225078
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.

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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
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