GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Rhodobacter johrii JA192

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  295 bits (756), Expect = 2e-84
 Identities = 172/498 (34%), Positives = 282/498 (56%), Gaps = 15/498 (3%)

Query: 11  LSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEG 70
           +++P L +  V + F  V  L  V    + G+++ L+GENG GKST +KI++G   P  G
Sbjct: 1   MTEPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAG 60

Query: 71  QLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDR 130
           +++++G P    S+ EA AAG+  ++Q+ +L   ++V EN+ L  EL     +     D 
Sbjct: 61  EVLLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGREL-----KRGPFLDH 115

Query: 131 RVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSL 190
           R + A + R LE +    +   +   +  L +  RQ+V IA+A+  +A+ +IMDEPT  L
Sbjct: 116 RAMQAESRRLLERLHCAVDPRAR---VSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVL 172

Query: 191 TQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQ 250
           T +E D L+  +  LRA G  +L+ SHKLDE   I   V VLRDG+++   P    ++ +
Sbjct: 173 THRETDTLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDR 232

Query: 251 ISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGR 310
           ++E M GR LS     +S+ A + VL+V G T  G   D SF L  GE+LG  GL+ SGR
Sbjct: 233 MAETMVGRELSGLFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGR 292

Query: 311 NELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNV 370
            EL   + G+ PA +G+V ++G  +   + S A+   + Y+ EDR  +GL L KP+ +N+
Sbjct: 293 TELMEGIVGLRPA-TGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENL 351

Query: 371 ITAMISSLRDRFGQ--IDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRW 428
               +    DRFG+  ID+   +    Q + +  I          SLSGGNQQ++L+ + 
Sbjct: 352 TLLAL----DRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKT 407

Query: 429 LAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMK 488
           +  +PRV+I+  PT G+DVG+K  IY  + RL+  G  +I++S +LPE++   +R+++M 
Sbjct: 408 MLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMS 467

Query: 489 KGHVSAEYRADELSEADL 506
            G ++ E   + ++E ++
Sbjct: 468 AGRIAGEVEGEAITEENI 485



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 73/267 (27%), Positives = 122/267 (45%), Gaps = 42/267 (15%)

Query: 8   SAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67
           S+P  +P LEV G+    T    +R  S + +RG++    G  G G++ L++ I G +P 
Sbjct: 250 SSPAPEPVLEVAGL----TVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGLRPA 305

Query: 68  DEGQLVIEG--VPHARLSALEALAAGIETVYQDLS---LLPNMSVAENVALTS------- 115
             G++ +EG  +PHA +SA  A AAG+  + +D     LL    + EN+ L +       
Sbjct: 306 T-GEVRMEGSPLPHASVSA--ARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDRFGRV 362

Query: 116 --ELATHEGRLART---FDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAI 170
             + A  E  L +    FD RV      R + A  L G ++              Q + +
Sbjct: 363 LIDKAAEERALTQAISDFDIRV----GDRGISAGSLSGGNQ--------------QKLLL 404

Query: 171 ARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVI 230
           A+ + +E + VI+DEPT  +       +   +A L A+G +V+ VS +L E   +   V+
Sbjct: 405 AKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVV 464

Query: 231 VLRDGQKMAQGPIAEFTKAQISELMTG 257
           V+  G+   +      T+  I  L  G
Sbjct: 465 VMSAGRIAGEVEGEAITEENIVRLAMG 491


Lambda     K      H
   0.319    0.135    0.376 

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: 591
Number of extensions: 34
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: 515
Length of database: 499
Length adjustment: 34
Effective length of query: 481
Effective length of database: 465
Effective search space:   223665
Effective search space used:   223665
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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