Alignments for a candidate for nupA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_05166 H281DRAFT_05166 nucleoside ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Burk376:H281DRAFT_05166
          Length = 533

 Score =  343 bits (879), Expect = 1e-98
 Identities = 200/492 (40%), Positives = 299/492 (60%), Gaps = 8/492 (1%)

Query: 12  VTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLEN 71
           +TK++    AND V L +  GEIHA+LGENGAGKSTLM ++ G + P  GE+  +G+  +
Sbjct: 30  ITKQYPAVRANDDVTLIVAPGEIHAVLGENGAGKSTLMKVIYGAVRPDAGEIQWEGEAVD 89

Query: 72  IDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSERYG 131
           I SP+ A  LGIGMV QHF L +  TV ENI L  +       DLK   K+I E+S  YG
Sbjct: 90  IASPAAARKLGIGMVFQHFSLFETLTVGENIALALDEP----FDLKALSKRIREVSADYG 145

Query: 132 LSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKE 191
           L ++P   +  ++VG++QRVEI++ L +   +LI DEPT+VLTP  + +L   ++ L  E
Sbjct: 146 LDIDPQRHVHSLTVGERQRVEIVRCLLQNPRLLIMDEPTSVLTPQAVRKLFATLRRLAAE 205

Query: 192 GKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEKAA 251
           G SI+ I+HKLDEI+ + D  TV+R G+    V+  ++T+  LA+LMVG S+   T +  
Sbjct: 206 GCSILYISHKLDEIQELCDTATVMRGGRVTGHVKPKEETHASLAQLMVGHSLPDYTRR-E 264

Query: 252 AQPKDVVLEIKDLNI-KESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTK 310
             P  V+L++K L++  +      ++ +S  V AGEI G+AG+ GNGQ EL+ A++G  +
Sbjct: 265 HNPGAVLLDVKALSVTSDDPFGTSLENVSFAVHAGEIFGIAGVSGNGQAELLSALSGEKR 324

Query: 311 -VDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMS 369
            + + ++ +  K               G VPE+R   G V  MT++EN AL T ++  M 
Sbjct: 325 GLRADAVTICGKPAGRLGAGGRRALGFGFVPEERLGRGAVPAMTLSEN-ALLTAHRQKMV 383

Query: 370 KYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQ 429
           K G+++   + + AR  +E FDVR  G    A SLSGGN QK I+ REI + P +L+V+Q
Sbjct: 384 KSGWINSGAMRAFARRCIEAFDVRCGGSEALAQSLSGGNLQKYIMGREILQAPKVLVVAQ 443

Query: 430 PTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPET 489
           PT G+DVGA  +I ++L+     G A+LVIS EL+E+ ++ DRIAV+  G++  + +   
Sbjct: 444 PTWGVDVGAAAFIRQQLLDLSASGVAILVISEELEELFDICDRIAVLAGGRLSPVRATGA 503

Query: 490 TTKQELGILMVG 501
           T  +E+G  M G
Sbjct: 504 TNAEEIGRWMAG 515



 Score = 87.8 bits (216), Expect = 9e-22
 Identities = 77/268 (28%), Positives = 127/268 (47%), Gaps = 17/268 (6%)

Query: 242 SVSFITEKAAAQP----KDVVLEIKDLNIKESRGSLKVKG-LSLDVRAGEIVGVAGIDGN 296
           S SF ++ AAAQP    +     +    I +   +++    ++L V  GEI  V G +G 
Sbjct: 2   SDSFYSDGAAAQPATRPEQAAPRLMLKGITKQYPAVRANDDVTLIVAPGEIHAVLGENGA 61

Query: 297 GQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAE 356
           G++ L+K I G  + D+G I+   + +    P    +  +G V +      L   +TV E
Sbjct: 62  GKSTLMKVIYGAVRPDAGEIQWEGEAVDIASPAAARKLGIGMVFQ---HFSLFETLTVGE 118

Query: 357 NIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAR 416
           NIAL    +P        D   ++   RE+  ++ +          SL+ G +Q+  I R
Sbjct: 119 NIAL-ALDEP-------FDLKALSKRIREVSADYGL-DIDPQRHVHSLTVGERQRVEIVR 169

Query: 417 EIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVI 476
            + +NP LLI+ +PT  L   A+  +   L +   EG ++L IS +LDEI  + D   V+
Sbjct: 170 CLLQNPRLLIMDEPTSVLTPQAVRKLFATLRRLAAEGCSILYISHKLDEIQELCDTATVM 229

Query: 477 HDGQIQGIVSPETTTKQELGILMVGGNI 504
             G++ G V P+  T   L  LMVG ++
Sbjct: 230 RGGRVTGHVKPKEETHASLAQLMVGHSL 257


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: 621
Number of extensions: 29
Number of successful extensions: 9
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: 533
Length adjustment: 35
Effective length of query: 471
Effective length of database: 498
Effective search space:   234558
Effective search space used:   234558
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