Alignments for a candidate for nupA in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Rhizobium leguminosarum bv. trifolii WSM1325

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_012760709.1 RLEG_RS34945 ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>NCBI__GCF_000023185.1:WP_012760709.1
          Length = 506

 Score =  315 bits (808), Expect = 2e-90
 Identities = 189/500 (37%), Positives = 291/500 (58%), Gaps = 11/500 (2%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           ++ +  ++K +G   AN  ++L++    IHA+LGENGAGKSTLM ++ G+ +P +GEV  
Sbjct: 5   LLSLRGISKSYGQIHANQAIDLDVAPQSIHAILGENGAGKSTLMKLIYGVEQPDDGEVIW 64

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
           +G    + SP++A   GIGMV QHF L +  TV ENI L   V  G   +LK   ++I  
Sbjct: 65  EGNSLRLASPAEARRNGIGMVFQHFSLFETLTVLENIRL---VVPGRKAELK---ERIRT 118

Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185
           L   +GL V+P A +  +SVG++QRVEI+++L     +LI DEPT+VL P  + +L   +
Sbjct: 119 LGREFGLEVDPLAHVHALSVGERQRVEIIRSLMTNPKLLILDEPTSVLPPQLVEKLFDTL 178

Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245
           + L   G SI+LI+HKL+EIRA+ DR T++R G+    V+  +    +LA +M+GR +  
Sbjct: 179 RRLRDGGVSILLISHKLEEIRAICDRATILRGGRVTGDVDPREHDAHDLARMMIGREMPA 238

Query: 246 ITEKAAAQPKDVVLEIKDLNIK-ESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
                     +  LEI  L+ + +   ++ + G+SL+VRAGEI+G+AGI GNGQ EL   
Sbjct: 239 PISALPLSGGEKRLEIIGLDYQPDDPFAVPLSGISLEVRAGEILGIAGISGNGQGELAAL 298

Query: 305 ITG---LTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361
           I+G   L +     I +   D+               VPEDR   G V EM++  N +L 
Sbjct: 299 ISGETVLGRDQRDRIYMMEMDVGRLDAAARRTLGFAFVPEDRLGRGAVPEMSLVLN-SLL 357

Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421
           T +   + ++G +D  +  +   + + + DVR  G    A +LSGGN QK I+ REI  +
Sbjct: 358 TAHPLKLLRHGLVDKARALAFTHDCIRQNDVRTPGPDAEAGTLSGGNLQKFIVGREIMLS 417

Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481
           P LL ++QPT G+D+GA   I  RL+  R++G A+LVIS EL+E+  + D I V+H G++
Sbjct: 418 PKLLFLAQPTWGVDIGAASAIRSRLVALRNQGMAILVISEELEELFELCDSIQVLHHGRL 477

Query: 482 QGIVSPETTTKQELGILMVG 501
              ++   T  +E+G  M+G
Sbjct: 478 SPPLATRDTKPEEIGRHMIG 497



 Score = 40.8 bits (94), Expect = 1e-07
 Identities = 45/233 (19%), Positives = 94/233 (40%), Gaps = 16/233 (6%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSG-------------LLEPSEGEVHVKGKLEN 71
           ++LE++ GEI  + G +G G+  L  ++SG             ++E   G +    +   
Sbjct: 272 ISLEVRAGEILGIAGISGNGQGELAALISGETVLGRDQRDRIYMMEMDVGRLDAAARRTL 331

Query: 72  IDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSERYG 131
             +      LG G V +  +++++      + L           L      I +   R  
Sbjct: 332 GFAFVPEDRLGRGAVPEMSLVLNSLLTAHPLKLLRHGLVDKARALAFTHDCIRQNDVR-- 389

Query: 132 LSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKE 191
            +  PDA    +S G  Q+  + + +     +L   +PT  +     + +   +  L  +
Sbjct: 390 -TPGPDAEAGTLSGGNLQKFIVGREIMLSPKLLFLAQPTWGVDIGAASAIRSRLVALRNQ 448

Query: 192 GKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244
           G +I++I+ +L+E+  + D I V+  G+    +   D   +E+   M+G   S
Sbjct: 449 GMAILVISEELEELFELCDSIQVLHHGRLSPPLATRDTKPEEIGRHMIGAQAS 501


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: 619
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: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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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Protein sequences (fasta format)
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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