GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Caulobacter crescentus NA1000

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 CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  285 bits (728), Expect = 4e-81
 Identities = 176/502 (35%), Positives = 275/502 (54%), Gaps = 6/502 (1%)

Query: 5   TVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVH 64
           T++ +  V+K F    A D+V+L +  GE+HALLGENGAGKSTL+ ILS       G V 
Sbjct: 2   TLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVT 61

Query: 65  VKGK-LENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123
             G+ L+  D+P +   LGI  ++Q F L    +V EN+ LG E  +   +D    +   
Sbjct: 62  FAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADA 121

Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183
             L    GL + PDA +R ++V +QQ VEI K +   A ++I DEPTA L+  E+  L  
Sbjct: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181

Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV 243
           I+  L     S+I ++H+L E++A+ DR TV+R G+ + + ++ D    ++  LMVGR V
Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241

Query: 244 SFITEKAAAQPKDVVLEIKDLNIKESRGSLK--VKGLSLDVRAGEIVGVAGIDGNGQTEL 301
            F   K    P  VVL+++ +     R S    ++ +S   R GEIVG+AG+ G G+T+L
Sbjct: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301

Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361
            + I G   + +G + + +K +  + PR   +  +  VPEDR + G  L+ ++  N++L 
Sbjct: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361

Query: 362 TYYKPPMSKYG-FLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDR 420
           +     +S  G ++D            ++  ++ A    +   LSGGNQQK ++ R +  
Sbjct: 362 SL--KALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419

Query: 421 NPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQ 480
            P +LIV +PTRG+D+GA   +H+ L    D G AV+VIS EL E++ VSDRI V  +G 
Sbjct: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479

Query: 481 IQGIVSPETTTKQELGILMVGG 502
           I   +  +T T++ L   M  G
Sbjct: 480 IVADLDAQTATEEGLMAYMATG 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: 576
Number of extensions: 25
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 506
Length of database: 515
Length adjustment: 35
Effective length of query: 471
Effective length of database: 480
Effective search space:   226080
Effective search space used:   226080
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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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:

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:

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:

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:

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