Alignments for a candidate for fruK in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Phaeobacter inhibens BS107

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  360 bits (923), Expect = e-104
 Identities = 201/505 (39%), Positives = 319/505 (63%), Gaps = 12/505 (2%)

Query: 1   MTDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60
           MT+++P++ ++GI   FPGV+ALDGV LT+ PGEVHALMGENGAGKST++K L G+++ +
Sbjct: 1   MTEQSPVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD 60

Query: 61  AGSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKK 119
            G I+V  +P   +G LDA+  GI  ++QE++L   LSV EN+ LG   R  FG +DW +
Sbjct: 61  EGQIIVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAE 120

Query: 120 THEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANE 179
                   L ++ +   +  T +  +SIA QQ+V IARA+ ++AK +I DEPT+SL   E
Sbjct: 121 LEAKTNAILEKLKV-GFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAE 179

Query: 180 VRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGM 239
              LF ++  +++ GV I ++SH +++I++ITDR+++LR+GQ+   V T +T  + +  M
Sbjct: 180 KVVLFEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQM 239

Query: 240 MIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLG 299
           MIG+   +LS+  A     E+       ++V+GL        V+ ++ +GEVVGF GL+G
Sbjct: 240 MIGRK-LDLSRNEAHHELGEVA------LEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVG 292

Query: 300 SGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVR 359
           +GRTE+   L+G   P SG+  L+G +V I+ P+ A++  I+   E+R+ +G++  +  R
Sbjct: 293 AGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCR 352

Query: 360 QNILIALQATRGMFKPIPKKEAD-AIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418
            N+ +  Q       P     A+ AI D+Y  +L++R     + V NLSGGNQQK++IG+
Sbjct: 353 DNMTLP-QVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGK 411

Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
           WL+  P +LI+DEPTRGID+G+KAEI  ++ DLA+QG  V+ ISSE+ EV+ ++D I V 
Sbjct: 412 WLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRI-VA 470

Query: 479 KDRHKIAEIENDDTVSQATIVETIA 503
               +I      + V++  ++  I+
Sbjct: 471 MYSGRIMRTFTSEEVTEENLIAAIS 495



 Score = 76.3 bits (186), Expect = 2e-18
 Identities = 54/230 (23%), Positives = 107/230 (46%), Gaps = 17/230 (7%)

Query: 24  DGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAG 83
           + V+  +  GEV    G  GAG++ + + L G+    +GSI +DG         DA   G
Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332

Query: 84  IATVYQE---VNLCTNLSVGENVMLGHE---KRGPFGIDWKKTHEAAKKYLAQMGLESID 137
           I+ V ++     L   ++  +N+ L      K GPF  D       A+  +     + +D
Sbjct: 333 ISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVAD------GAEIAIFDQYRDKLD 386

Query: 138 PHTP-----LSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRD 192
             TP     + ++S   QQ + I + + +   VLI+DEPT  +D     ++  ++R +  
Sbjct: 387 IRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAA 446

Query: 193 SGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242
            G A++ +S  + ++  + DR+  + +G+ ++   +++   + LI  + G
Sbjct: 447 QGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISG 496


Lambda     K      H
   0.316    0.135    0.376 

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: 663
Number of extensions: 32
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: 513
Length of database: 503
Length adjustment: 34
Effective length of query: 479
Effective length of database: 469
Effective search space:   224651
Effective search space used:   224651
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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:

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