Alignments for a candidate for nupA in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Trichormus variabilis ATCC 29413

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_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  328 bits (841), Expect = 3e-94
 Identities = 184/479 (38%), Positives = 290/479 (60%), Gaps = 8/479 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           V++M  + KRF    A   VNL +  GE+HAL+GENGAGKSTLM IL+G     EGE+ +
Sbjct: 18  VLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIRI 77

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
            GK   I  P  A   GI +++Q   +    TVTENI +G+E+T+G  LD K  + +  +
Sbjct: 78  NGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSELTRGQFLDRKAMELEAQQ 137

Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185
           +    G S  P  ++  +++ +QQ+VEI + L   + IL+ DEPTA L+  E   L +++
Sbjct: 138 VLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEVI 197

Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV-S 244
           + L  +G +II I+H+++EI A+ADRI+V+R G+ I ++   + + Q L ++MVGRS+  
Sbjct: 198 RKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMMVGRSMQD 257

Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
           F   +  + P  VVLE++  NI + R   KV+  S  +RAGEI+G+AG+ G G+TE+ + 
Sbjct: 258 FYEHQRQSNPGPVVLEVR--NISDGR---KVQPASFQLRAGEILGLAGLVGAGRTEVSRL 312

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           I G  +  SG + L+ K +    P       +G+VPEDR   GL LEM+  +NI L    
Sbjct: 313 IFGADRKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMSSRKNIGLNRLK 372

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
           +   +  G +++  +N  A + +E F +R A   + A  LSGGNQQK ++AR +  NP +
Sbjct: 373 QD--ANLGIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQKLLLARWLAINPRV 430

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQG 483
           L++ +PTRG+D+GA   I++ +     +G A+L++S EL EI+ +SDR+ V+ +GQ+ G
Sbjct: 431 LMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLVMREGQLVG 489



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 63/249 (25%), Positives = 130/249 (52%), Gaps = 9/249 (3%)

Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317
           VLE++ +  K   G   ++G++L +  GE+  + G +G G++ L+K + G    D G I+
Sbjct: 18  VLEMQGI-AKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADEGEIR 76

Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377
           ++ K +    P    +  +  + ++ +   +   +TV ENI + +     +++  FLD  
Sbjct: 77  INGKGVKITDPGTARQAGINLIYQELN---VAPNLTVTENIFMGS----ELTRGQFLDRK 129

Query: 378 KINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVG 437
            +   A++++       A   +   +L+   QQ+  IAR +  N  +L++ +PT  L   
Sbjct: 130 AMELEAQQVLASLGASFAPTDI-VGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDR 188

Query: 438 AIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGI 497
             E + + + + R++G A++ IS  ++EI  ++DRI+V+ DGQ  G ++ E  + Q L  
Sbjct: 189 ETERLFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQ 248

Query: 498 LMVGGNINE 506
           +MVG ++ +
Sbjct: 249 MMVGRSMQD 257



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 60/217 (27%), Positives = 112/217 (51%), Gaps = 10/217 (4%)

Query: 26  NLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIGM 85
           + +L+ GEI  L G  GAG++ +  ++ G      GEV + GK   I SPS A  +GIG 
Sbjct: 287 SFQLRAGEILGLAGLVGAGRTEVSRLIFGADRKVSGEVFLNGKKLEIHSPSDAIAVGIGY 346

Query: 86  VHQHFMLVDAF---TVTENIILGNEVTKGINLDLK---TAKKKILELSERYGLSVEP-DA 138
           V +       F   +  +NI L N + +  NL +    +  K   +  E + + +   + 
Sbjct: 347 VPEDRKDQGLFLEMSSRKNIGL-NRLKQDANLGIVNWGSVNKIATDAVENFHIRLANLEI 405

Query: 139 LIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIILI 198
              D+S G QQ++ + + L     +L+ DEPT  +     +E+ +I+ +L  +G +I+++
Sbjct: 406 RAVDLSGGNQQKLLLARWLAINPRVLMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMV 465

Query: 199 THKLDEIRAVADRITVIRRGKSIDTVE--LGDKTNQE 233
           + +L EI  ++DR+ V+R G+ +  ++  +G +  QE
Sbjct: 466 SSELPEIVGLSDRVLVMREGQLVGELDNSIGKEITQE 502


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: 660
Number of extensions: 28
Number of successful extensions: 7
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: 506
Length of database: 517
Length adjustment: 35
Effective length of query: 471
Effective length of database: 482
Effective search space:   227022
Effective search space used:   227022
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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