Alignments for a candidate for xylK_Tm in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  285 bits (730), Expect = 2e-81
 Identities = 170/483 (35%), Positives = 271/483 (56%), Gaps = 14/483 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L+ + I KRF  V A D+V F+++  E+++L+GENGAGK+TL+ IL G    D G + +
Sbjct: 15  VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G  +   +P  A   G+ ++HQ   L DN+TV ENI L  E + G    L  R      
Sbjct: 75  FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLG----LGLRAGP--A 128

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
             R + L +    K  P+A V  LT  +RQ VEI KAL ++ RI+ +DEPT+ LT +E++
Sbjct: 129 KARIRALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESD 188

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            LF  +    +RG+SV+F+SH+L EVM ISDR++V+R GK + E +  + D D +  +MV
Sbjct: 189 ALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMV 248

Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDK-----VKNVSFEVRKGEVLGFAGLVGAGRT 308
           G +V        T PG   L++R++          +++VS ++  G++ G AG+ G G+ 
Sbjct: 249 GADVVPAKFAANT-PGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQA 307

Query: 309 ETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIV 368
               LV G+   +SG + +NG      +P +AI  GI  IPEDR   G +    + +N +
Sbjct: 308 ALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAI 367

Query: 369 LPS-LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427
           L +   + S  G  LD R   + ++  +    ++ P        LSGGN QK++L + L 
Sbjct: 368 LETYATRFSHRGW-LDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLE 426

Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEG 487
            +  I++ ++P RG+D+GA   +H  + +  A+G AV++IS +L EI+ LSD I V+ EG
Sbjct: 427 QSPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEG 486

Query: 488 EIT 490
            ++
Sbjct: 487 RLS 489



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 59/206 (28%), Positives = 105/206 (50%), Gaps = 7/206 (3%)

Query: 286 NVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGI 345
           +VSF++  GEV+   G  GAG+T  M ++FG    ++G + + G  +    P  A+  G+
Sbjct: 33  DVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPLPPGAPRAALDGGV 92

Query: 346 GLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSI 405
           G++ +   L      +TV +NI L     +   GL L     +       ++  +K    
Sbjct: 93  GMVHQHFTLAD---NLTVWENITLGVEPLL---GLGLRAGPAKARIRALAEQFHLKVDPN 146

Query: 406 YQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVI 465
            +++  L+ G +Q+V + K L  +A ILI DEPT  +       +   +RE   +G +VI
Sbjct: 147 AKVSR-LTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATLREAINRGLSVI 205

Query: 466 MISSELPEILNLSDRIVVMWEGEITA 491
            IS +L E++ +SDR++V+  G++ A
Sbjct: 206 FISHKLHEVMAISDRVLVLRHGKLVA 231



 Score = 73.6 bits (179), Expect = 2e-17
 Identities = 58/240 (24%), Positives = 112/240 (46%), Gaps = 16/240 (6%)

Query: 32  NVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGI 91
           +V  ++   +I  L G +G G++ L  +++G++ P +G + +NG      SP +A   GI
Sbjct: 285 HVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGI 344

Query: 92  SVIHQELNLCDNMT---VAENIFLAYEAVRGQKRT-LSSRVDENYMYTRSKELLDLIGAK 147
           + I ++ +    +    + EN  L   A R   R  L  R   ++    +K ++     +
Sbjct: 345 ARIPEDRHKTGTIADFDLTENAILETYATRFSHRGWLDWRAARDF----AKTVITGYDVR 400

Query: 148 F-SPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRG 206
              PD  +R L+    Q + + + L + P+II  ++P   L +     + E +    +RG
Sbjct: 401 CPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGLDIGAVTYVHEQLAKACARG 460

Query: 207 ISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREVEFFPHGIET 266
            +V+ +S  LDE+M++SD I V+ +G+      +G    + +   M G       HG +T
Sbjct: 461 AAVLLISEDLDEIMQLSDVIHVISEGRLSPGFARGSKQPEELGAWMAG-------HGFDT 513


Lambda     K      H
   0.319    0.138    0.381 

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: 584
Number of extensions: 23
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: 520
Length of database: 522
Length adjustment: 35
Effective length of query: 485
Effective length of database: 487
Effective search space:   236195
Effective search space used:   236195
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 (21.7 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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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
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