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

GapMind for catabolism of small carbon sources

Aligments 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:

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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