Alignments for a candidate for xylG in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Phaeobacter inhibens BS107

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  283 bits (725), Expect = 8e-81
 Identities = 160/482 (33%), Positives = 274/482 (56%), Gaps = 13/482 (2%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           + P+L +++I KRF  V A   VS + +PGEV A++GENGAGK+TLM I+ G Y  D G 
Sbjct: 12  LTPVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGG 71

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           +   G  +    P  A++ G+  V Q  ++ DNL+V ENI +G E   G+ +      + 
Sbjct: 72  VELFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPA-KA 130

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
             + + E+F +++DP  K+ + ++  +Q VEI +A+Y+ A++LILDEPT+ LT +E++ L
Sbjct: 131 RIRALAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDAL 190

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F  ++    +G+++IFISH+L E+  I D+V VLR G+ +      +   + +  +MVG 
Sbjct: 191 FATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGA 250

Query: 241 KL--EKFYIKEAHEPGEVVLEVKNL------SGERFENVSFSLRRGEILGFAGLVGAGRT 292
            +   KF    A+ PG  +L+++++      +     +VS  L  G+I G AG+ G G+ 
Sbjct: 251 DVVPAKF---AANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQA 307

Query: 293 ELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVS 352
            L + + G    + G + + G       P +AI  GI  +PEDR K G I    +  N  
Sbjct: 308 ALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAI 367

Query: 353 LPS-LDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411
           L +   R     ++ ++  ++ A   I  +D+R   PD ++  LSGGN QK++L + L  
Sbjct: 368 LETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQ 427

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
            P+I++ ++P RG+D+GA   ++  +++    G  V++IS +L E++Q+SD I V+S G+
Sbjct: 428 SPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGR 487

Query: 472 LA 473
           L+
Sbjct: 488 LS 489



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 72/248 (29%), Positives = 122/248 (49%), Gaps = 21/248 (8%)

Query: 257 VLEVKNLSGERF------ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIY 310
           VL ++N++ +RF      ++VSF L  GE++   G  GAG+T LM  +FG      G + 
Sbjct: 15  VLRLQNIT-KRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73

Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSL---PSLDR-IKKGPFIS 366
           + G  +    P  A++ G+G+V    +   L   +++  N++L   P L   ++ GP  +
Sbjct: 74  LFGAPLPPGAPRAALDGGVGMV---HQHFTLADNLTVWENITLGVEPLLGLGLRAGP--A 128

Query: 367 FKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGID 426
             R + LA+      D     P+ KV  L+ G +Q+V + K L    +ILILDEPT  + 
Sbjct: 129 KARIRALAEQFHLKVD-----PNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLT 183

Query: 427 VGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKV 486
                 ++  + +    G+ VI IS +L EV+ +SDR+ V+  GKL       +   + +
Sbjct: 184 PQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDAL 243

Query: 487 MKLAAGLE 494
             L  G +
Sbjct: 244 AALMVGAD 251


Lambda     K      H
   0.318    0.138    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: 535
Number of extensions: 29
Number of successful extensions: 7
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: 494
Length of database: 522
Length adjustment: 34
Effective length of query: 460
Effective length of database: 488
Effective search space:   224480
Effective search space used:   224480
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 (21.7 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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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