Alignments for a candidate for nupA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Phaeobacter inhibens BS107

Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Phaeo:GFF2651
          Length = 522

 Score =  371 bits (953), Expect = e-107
 Identities = 206/496 (41%), Positives = 300/496 (60%), Gaps = 2/496 (0%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           V+++ ++TKRFG   AND V+ +L  GE+ ALLGENGAGK+TLMNIL G      G V +
Sbjct: 15  VLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVEL 74

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
            G      +P  A + G+GMVHQHF L D  TV ENI LG E   G+ L    AK +I  
Sbjct: 75  FGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIRA 134

Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185
           L+E++ L V+P+A +  ++VG++QRVEILK LYR A ILI DEPTAVLTP E   L   +
Sbjct: 135 LAEQFHLKVDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFATL 194

Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245
           +  I  G S+I I+HKL E+ A++DR+ V+R GK +   +  D  +  LA LMVG  V  
Sbjct: 195 REAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV-V 253

Query: 246 ITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI 305
             + AA  P   +L+++D+    +  S  ++ +SLD+ AG+I G+AG+ GNGQ  L   +
Sbjct: 254 PAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLV 313

Query: 306 TGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYK 365
           +GL    SGS+ L+        PR+     +  +PEDRH+ G + +  + EN  L+T Y 
Sbjct: 314 SGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILET-YA 372

Query: 366 PPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLL 425
              S  G+LD+      A+ ++  +DVR  G       LSGGN QK I+ R ++++P ++
Sbjct: 373 TRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQII 432

Query: 426 IVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIV 485
           + +QP RGLD+GA+ Y+H++L +A   G AVL+IS +LDEI+ +SD I VI +G++    
Sbjct: 433 LANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGF 492

Query: 486 SPETTTKQELGILMVG 501
           +  +   +ELG  M G
Sbjct: 493 ARGSKQPEELGAWMAG 508



 Score = 82.4 bits (202), Expect = 4e-20
 Identities = 66/241 (27%), Positives = 114/241 (47%), Gaps = 9/241 (3%)

Query: 265 NIKESRGSLKVKG-LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDI 323
           NI +  GS+     +S D+  GE++ + G +G G+T L+  + G    D+G ++L    +
Sbjct: 20  NITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVELFGAPL 79

Query: 324 TNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHA 383
               PR   +  VG V +      L   +TV ENI L      P+   G L      +  
Sbjct: 80  PPGAPRAALDGGVGMVHQ---HFTLADNLTVWENITLGV---EPLLGLG-LRAGPAKARI 132

Query: 384 RELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIH 443
           R L E+F ++        S L+ G +Q+  I + + R+  +LI+ +PT  L     + + 
Sbjct: 133 RALAEQFHLK-VDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALF 191

Query: 444 KRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGN 503
             L +A + G +V+ IS +L E++ +SDR+ V+  G++        T    L  LMVG +
Sbjct: 192 ATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGAD 251

Query: 504 I 504
           +
Sbjct: 252 V 252


Lambda     K      H
   0.315    0.135    0.365 

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: 615
Number of extensions: 25
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: 506
Length of database: 522
Length adjustment: 35
Effective length of query: 471
Effective length of database: 487
Effective search space:   229377
Effective search space used:   229377
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: 42 (22.0 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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Candidates (tab-delimited)
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