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 GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  260 bits (664), Expect = 1e-73
 Identities = 157/478 (32%), Positives = 256/478 (53%), Gaps = 9/478 (1%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ ++ IT  F  V A D V   L+PGEV AL+GENGAGK+T++  L G Y  + G + 
Sbjct: 14  PVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           + G P        A + G+  V+Q   L  NL+V EN+ LG E     G+         +
Sbjct: 74  LFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIR 133

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
               Q  L+ +DP+  +S +++  +Q V I +A+  +A++LILDEPT+ L   E   LFA
Sbjct: 134 ALAEQFHLK-VDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFA 192

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
            +R+  + G++++F+SH L ++  I+DR+ +LR+G+ + E  T DT  D L  +M+G   
Sbjct: 193 TLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV 252

Query: 246 AELSQIGAKKARREITPGEKPIVDV--KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
                + AK A     P    + DV     G    +  V +D+  G++ G AG+ G+G+ 
Sbjct: 253 -----VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQA 307

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
            L  L+ G   P SG+ TLNG       P  A+   IA   E+R   G I D  + +N +
Sbjct: 308 ALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAI 367

Query: 364 IALQATRGMFKP-IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422
           +   ATR   +  +  + A       +   +VR   PD  ++ LSGGN QK+++GR L  
Sbjct: 368 LETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQ 427

Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480
            P++++ ++P RG+DIGA   + + +    ++G  V+ IS +L+E+++LSD I V+ +
Sbjct: 428 SPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISE 485



 Score = 87.8 bits (216), Expect = 9e-22
 Identities = 66/239 (27%), Positives = 122/239 (51%), Gaps = 10/239 (4%)

Query: 262 PGEKPIVDVKGLGKK-GTI---NPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDS 317
           PG  P++ ++ + K+ G++   + V  D++ GEV+   G  G+G+T L  +L+G    D+
Sbjct: 10  PGLTPVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADT 69

Query: 318 GTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIP 377
           G   L G  +    P  AL   +    ++     +  +LTV +NI + ++   G+   + 
Sbjct: 70  GGVELFGAPLPPGAPRAALDGGVGMVHQHFT---LADNLTVWENITLGVEPLLGL--GLR 124

Query: 378 KKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGID 437
              A A +    ++ +++  DP+  V  L+ G +Q+V I + L     +LILDEPT  + 
Sbjct: 125 AGPAKARIRALAEQFHLK-VDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLT 183

Query: 438 IGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQA 496
                 +   + +  ++G+ V+FIS +L EV+ +SD + VL+    +AE +  DT S A
Sbjct: 184 PQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDA 242



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 52/245 (21%), Positives = 107/245 (43%), Gaps = 11/245 (4%)

Query: 7   IVVMKGITIEFPGVK-ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           ++ ++ +T    G    L  V L L  G++  L G +G G++ +   ++G+    +GS+ 
Sbjct: 266 LLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLT 325

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLG-----HEKRGPFGIDW 117
           ++G         +A  AGIA + ++        +  + EN +L         RG   +DW
Sbjct: 326 LNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYATRFSHRG--WLDW 383

Query: 118 KKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDA 177
           +   + AK  +    +    P T +  +S    Q + + R +  + ++++ ++P   LD 
Sbjct: 384 RAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGLDI 443

Query: 178 NEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
             V  +   + K    G A+L +S  LD+I +++D + ++  G+            +EL 
Sbjct: 444 GAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGFARGSKQPEELG 503

Query: 238 GMMIG 242
             M G
Sbjct: 504 AWMAG 508


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: 609
Number of extensions: 35
Number of successful extensions: 8
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: 513
Length of database: 522
Length adjustment: 35
Effective length of query: 478
Effective length of database: 487
Effective search space:   232786
Effective search space used:   232786
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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Protein sequences (fasta format)
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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