GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Dyella japonica UNC79MFTsu3.2

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

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



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  304 bits (778), Expect = 6e-87
 Identities = 180/492 (36%), Positives = 286/492 (58%), Gaps = 13/492 (2%)

Query: 9   APLSQPF-LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67
           +P ++P  L+  G+ KRF    AL GV L+ + G+++ L+G+NG GKSTLIK+++G + P
Sbjct: 5   SPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERP 64

Query: 68  DEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLART 127
           D G + ++G   A  + +EA   GI TVYQ+++L PN+SVAEN  L +       RL R 
Sbjct: 65  DRGSVELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAEN--LYAGRYPRRRRL-RM 121

Query: 128 FDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPT 187
            D R +   A   L  + L  + +     +   P+A RQ+VAIARA+   A+ +I+DEPT
Sbjct: 122 IDWRQVRDGARSLLRQLHLELDVDAP---LGSYPVAIRQMVAIARALGVSARVLILDEPT 178

Query: 188 TSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT 247
           +SL + EV  L  V+A LR +G+ +LFV+H LD+ YA+   + VLRDG ++ +  +A+  
Sbjct: 179 SSLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLP 238

Query: 248 KAQISELMTGRHLSNERYRESAHA----QDIVLDVRGFTRAGQFSDVSFKLHGGEILGVT 303
            A +   M GR L      ++  A        +D +G    G+   V  ++  GE+LG+ 
Sbjct: 239 PAALVNAMVGRDLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLG 298

Query: 304 GLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLD 363
           GLL SGR ELAR L G+  A+ G++ + G+++ L+ P+DA    +   PE+R  +G+  +
Sbjct: 299 GLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAE 358

Query: 364 KPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRV 423
             +R+N++ A+    R  +  + R R   LA Q V+ L I    ++ PV  LSGGNQQ+V
Sbjct: 359 LSVRENIVLAL--QARQGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKV 416

Query: 424 LIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDR 483
           ++ RWL  +PR+LIL  PT G+DV +K  +   + R +  G+ ++ IS +  EL + CDR
Sbjct: 417 MLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDR 476

Query: 484 ILMMKKGHVSAE 495
           I +M++   + E
Sbjct: 477 IAVMRERRKAGE 488



 Score = 94.0 bits (232), Expect = 1e-23
 Identities = 73/248 (29%), Positives = 119/248 (47%), Gaps = 9/248 (3%)

Query: 268 SAHAQDIVLDVRG----FTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPA 323
           S  A+ +VL  RG    F        V   L  GE+  + G   +G++ L + L GV   
Sbjct: 5   SPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERP 64

Query: 324 QSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFG 383
             G V LDG+ IA  TP +A+R  IG V ++     L  +  + +N+        R R  
Sbjct: 65  DRGSVELDGRVIAPSTPMEAQRDGIGTVYQE---VNLCPNLSVAENLYAGRYPRRR-RLR 120

Query: 384 QIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTV 443
            ID  + +  A   +++L +    VD P+ S     +Q V I R L +  RVLIL  PT 
Sbjct: 121 MIDWRQVRDGARSLLRQLHLELD-VDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTS 179

Query: 444 GVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSE 503
            +D G    ++R++ +L +RG+ I+ ++  L ++    DRI +++ G    EY   +L  
Sbjct: 180 SLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPP 239

Query: 504 ADLYHALL 511
           A L +A++
Sbjct: 240 AALVNAMV 247



 Score = 62.0 bits (149), Expect = 5e-14
 Identities = 59/231 (25%), Positives = 106/231 (45%), Gaps = 12/231 (5%)

Query: 31  LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEG----VPHARLSALE 86
           L  V L  +RG++  L G  G G++ L +++ G    + G+L I G    + H   + + 
Sbjct: 282 LHPVDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVR 341

Query: 87  ALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGL 146
            LA   E    D  ++  +SV EN+ L   L   +G   R   R      A + ++A+G+
Sbjct: 342 GLALCPEERKTD-GIVAELSVRENIVLA--LQARQGW--RGMSRARQDELARQLVQALGI 396

Query: 147 PGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLR 206
                   T +  L    +Q V +AR + +E + +I+DEPT  +       L+A +    
Sbjct: 397 KAADI--ETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRA 454

Query: 207 AQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
             G+ VLF+S +  E       + V+R+ +K  + P    T+A++  ++ G
Sbjct: 455 HAGMAVLFISAETGELTRWCDRIAVMRERRKAGELP-GGSTEARVLAMIAG 504


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: 601
Number of extensions: 29
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 505
Length adjustment: 34
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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 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