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

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 Apr 09 2024. 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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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