GapMind for catabolism of small carbon sources

 

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

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3232
          Length = 513

 Score =  416 bits (1070), Expect = e-121
 Identities = 228/499 (45%), Positives = 326/499 (65%), Gaps = 12/499 (2%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPD--EGEI 61
           + E++ I K F GV AL G+ +    GE   + GENGAGKSTLMK+++GVY     +GEI
Sbjct: 7   LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKR-GIFIDYKKMYRE 120
           +++G+ +R     ++  AGIV + QEL ++  LSVAENIF+G E  R G  +DY  MY +
Sbjct: 67  LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAK 126

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A+  ++E    +++       Y    QQ+ EIA+A+ K+AK+LILDEPTSSLT  ETE L
Sbjct: 127 ADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVL 186

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
             +V+ LK +GVA I+ISH+L+E+  +CD V V+RDG +I T  +  L  + ++ +MVGR
Sbjct: 187 LGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGR 246

Query: 241 KLEKFYIKEAHEPGEVVLEVK--------NLSGERFENVSFSLRRGEILGFAGLVGAGRT 292
           KLE  Y +  H  GEV+ E +        N   +R ++VSF LRRGEILG AGLVGAGRT
Sbjct: 247 KLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRT 306

Query: 293 ELMETIFG-FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV 351
           EL+  IFG +  K   E+++EG+ ++I  P DAI  G+G+VPEDRK+ G++ ++ +  N+
Sbjct: 307 ELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNI 366

Query: 352 SLPSLDRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLAL 411
           +L +LD       I  +RE    +  I    ++ A P   +  LSGGNQQK VLAK L  
Sbjct: 367 TLATLDHYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLLA 426

Query: 412 KPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGK 471
           +PK+LILDEPTRG+DVGAKAEIYR++ +LA +GV ++++SSE+PEVL M+DR+ VM  G+
Sbjct: 427 RPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGR 486

Query: 472 LAGIIDAKEASQEKVMKLA 490
           L G    +  +QE+V+  A
Sbjct: 487 LRGDFPNQGLTQEQVLAAA 505



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 61/226 (26%), Positives = 105/226 (46%), Gaps = 6/226 (2%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRG--GEIYIEGKRVEINHPLDAIE 326
           + +   LR GE LG  G  GAG++ LM+ + G  P     GEI  +G+ +      D+  
Sbjct: 24  DGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEILWQGQPLRARSVRDSER 83

Query: 327 QGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIKTFDIRPA 386
            GI ++ ++   L L+  +S+  N+ L   +  + G  + +      AD  ++   +   
Sbjct: 84  AGIVIIHQE---LMLVPQLSVAENIFLGH-EITRPGGRMDYDAMYAKADALLQELGLHDV 139

Query: 387 YPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVG 446
                 ++  GG+QQ   +AK LA + K+LILDEPT  +       +  I+  L + GV 
Sbjct: 140 NVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVLLGIVEDLKRRGVA 199

Query: 447 VIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
            I IS +L EV ++ D + V+  G+        E   + ++ L  G
Sbjct: 200 CIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVG 245


Lambda     K      H
   0.318    0.138    0.385 

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: 684
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: 494
Length of database: 513
Length adjustment: 34
Effective length of query: 460
Effective length of database: 479
Effective search space:   220340
Effective search space used:   220340
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: 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