GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Pseudomonas fluorescens FW300-N2E3

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 AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20820
          Length = 517

 Score =  267 bits (683), Expect = 6e-76
 Identities = 162/474 (34%), Positives = 269/474 (56%), Gaps = 10/474 (2%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           ++L L +GE+ AL GENGAGKSTL  I+ GL+ P+ G++  +G+     S ++A  LGI 
Sbjct: 27  IDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEELGIR 86

Query: 85  MVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSERYGL-SVEPDALIRDI 143
           MV Q   L+   +V EN+ L N  + G  +  K  +K  +    + GL +++PD L+ ++
Sbjct: 87  MVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIAAMAQVGLDAIDPDTLVGEL 146

Query: 144 SVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIILITHKLD 203
            +G QQ VEI + L     +LI DEPTA+LT  E+  L + +  L   G +II I+H+L+
Sbjct: 147 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAIIYISHRLE 206

Query: 204 EIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEKAAAQPKDVVLEIKD 263
           E+  VA RI V+R G  +    + +  +++L  LMVGR +    E     P+ +      
Sbjct: 207 ELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELG---EHIDLGPRHI--GAPA 261

Query: 264 LNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHN--K 321
           L +K    S KV+ +S +VR+GEI G++G+ G G+TEL++ I G    DSG++ L +  +
Sbjct: 262 LTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADAADSGTVALGSPAQ 321

Query: 322 DITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINS 381
            ++ + P       +  + EDR  +GL+L  +++ NIAL     P +S  G ++     +
Sbjct: 322 VVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGN--MPVISSGGIVNSGDEMA 379

Query: 382 HARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEY 441
            A+  ++   +R +      S LSGGNQQK +I R ++R   +L+  +PTRG+DVGA   
Sbjct: 380 LAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLLFDEPTRGIDVGAKFD 439

Query: 442 IHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQEL 495
           I+  L +   +GKA++V+S +L E++ + DRI V+  G++      ++ T+ +L
Sbjct: 440 IYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDL 493



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 58/230 (25%), Positives = 109/230 (47%), Gaps = 7/230 (3%)

Query: 277 GLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSV 336
           G+ L +  GE++ + G +G G++ L K I GL    +G ++   +D       +  E  +
Sbjct: 26  GIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGRDYRPGSRTQAEELGI 85

Query: 337 GHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAG 396
             V ++ +   L+  ++VAEN+ L        S  G++   ++   A   M +  +    
Sbjct: 86  RMVMQELN---LLPTLSVAENLFLDNL----PSNGGWISRKQLRKAAIAAMAQVGLDAID 138

Query: 397 EWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAV 456
                  L  G+QQ   IAR +  +  +LI+ +PT  L    +E + +++ + +  G A+
Sbjct: 139 PDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVAI 198

Query: 457 LVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506
           + IS  L+E+  V+ RIAV+ DG +  +        ++L  LMVG  + E
Sbjct: 199 IYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELGE 248


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: 644
Number of extensions: 36
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: 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 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