Alignments for a candidate for nupA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Halomonas desiderata SP1

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 WP_086510989.1 BZY95_RS16555 L-arabinose ABC transporter ATP-binding protein AraG

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_002151265.1:WP_086510989.1
          Length = 497

 Score =  265 bits (677), Expect = 3e-75
 Identities = 160/497 (32%), Positives = 275/497 (55%), Gaps = 14/497 (2%)

Query: 4   ETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEV 63
           E  ++   ++  F    A D V+     G++HAL+GENGAGKSTL+ +LSG+  PSEG +
Sbjct: 3   EPYLRFDGISMVFPGVRALDGVSFGAHAGQVHALMGENGAGKSTLLKVLSGVNHPSEGAL 62

Query: 64  HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123
            + G+     +  +A   GI +++Q   L    TV EN++LG   T+   +  +  +++ 
Sbjct: 63  WIDGERHVFANAREALAQGIAIIYQELTLSPNMTVAENLLLGQLPTRHGFIKRRQLRERA 122

Query: 124 LELSERYGLS-VEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELM 182
           L +    G   + P   +R++S+GQQQ +EI + L R A I+ FDEPT+ L+  E  +L 
Sbjct: 123 LAILADLGEGDIHPSTKVRELSIGQQQMIEIGRALLRNARIIAFDEPTSSLSVQETRQLK 182

Query: 183 QIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDT-VELGDKTNQELAELMVGR 241
           +I+  L +EG+ ++ +TH+++E+  + D +TV R GK I T   L    +  L   MVGR
Sbjct: 183 RIISRLREEGRVVLYVTHRMEEVFDMCDAVTVFRDGKHIRTHASLAALDHDTLVSEMVGR 242

Query: 242 SVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTEL 301
            +  +      +  +V+LEI  +   E RG LK   +S +VR GE+ G+ G+ G G++EL
Sbjct: 243 DIEDVYGYRERERGEVILEIDAI---EGRG-LKAP-VSFEVRRGEVFGLFGLVGAGRSEL 297

Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAEN--IA 359
           ++ + G  +  +G ++   +      P +     +   PEDR   G+    +VA+N  I+
Sbjct: 298 MRLVCGAERASAGEVRFQGQARRFASPGEAIRMGIAMCPEDRKSQGIFPVASVADNLNIS 357

Query: 360 LQTYYKPPMSKYGFL-DYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREI 418
            + +++    ++G L D  +  ++A   ++   ++  G   +  +LSGGNQQK I+AR +
Sbjct: 358 CRRFFR----RWGVLRDTRRERANAEAYIQRLSIKTPGPRTAIGTLSGGNQQKVILARWL 413

Query: 419 DRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHD 478
               +L +V +PTRG+DVGA   I+  L    ++GK+V+VIS +L E+ ++ DRI V+ D
Sbjct: 414 AEKIELFVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVVISSDLAEVSSICDRIGVMRD 473

Query: 479 GQIQGIVSPETTTKQEL 495
           G +  +V     T++ L
Sbjct: 474 GALVEVVPRHEATQERL 490



 Score = 90.1 bits (222), Expect = 2e-22
 Identities = 60/220 (27%), Positives = 106/220 (48%), Gaps = 7/220 (3%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           V+ E+++GE+  L G  GAG+S LM ++ G    S GEV  +G+     SP +A  +GI 
Sbjct: 274 VSFEVRRGEVFGLFGLVGAGRSELMRLVCGAERASAGEVRFQGQARRFASPGEAIRMGIA 333

Query: 85  MVHQHFMLVDAFTVTE-----NIILGNEVTK-GINLDLKTAKKKILELSERYGLSVE-PD 137
           M  +       F V       NI       + G+  D +  +       +R  +    P 
Sbjct: 334 MCPEDRKSQGIFPVASVADNLNISCRRFFRRWGVLRDTRRERANAEAYIQRLSIKTPGPR 393

Query: 138 ALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIIL 197
             I  +S G QQ+V + + L    ++ + DEPT  +      ++  ++ +L ++GKS+++
Sbjct: 394 TAIGTLSGGNQQKVILARWLAEKIELFVVDEPTRGIDVGARRDIYTLLFDLTEQGKSVVV 453

Query: 198 ITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAEL 237
           I+  L E+ ++ DRI V+R G  ++ V   + T + L  L
Sbjct: 454 ISSDLAEVSSICDRIGVMRDGALVEVVPRHEATQERLLGL 493


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: 581
Number of extensions: 33
Number of successful extensions: 8
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: 497
Length adjustment: 34
Effective length of query: 472
Effective length of database: 463
Effective search space:   218536
Effective search space used:   218536
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 Apr 09 2024. 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 2024 update 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