Alignments for a candidate for HSERO_RS03640 in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Dyella japonica UNC79MFTsu3.2

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  393 bits (1009), Expect = e-114
 Identities = 221/498 (44%), Positives = 310/498 (62%), Gaps = 8/498 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           +LQ RG+ K FGATLAL  + L +R GE+HALMG+NGAGKSTL+K+L+GV  PD+G + L
Sbjct: 12  VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGS-ELRTRLGLIDHAAMRSRT 124
           DGR +A   P  ++  GI  +YQE+ + PN+SVA N++ G    R RL +ID   +R   
Sbjct: 72  DGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDGA 131

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
            ++LRQL          G   +A +Q V IARAL   +R++I+DEPT++L E E  +LF 
Sbjct: 132 RSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFR 191

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244
           V+ +LR+ G+AI++++H + +VYA++DR+TVLRDG  VGE    ++    +V  MVGR L
Sbjct: 192 VIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRDL 251

Query: 245 SEFY--QHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRTEL 301
                   +R  P DA   P  +  + L   GK+ P    VR GE+LG  GL+G+GRTEL
Sbjct: 252 PTVAGADAERAPPPDA---PPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGRTEL 308

Query: 302 ARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMN 361
           ARLLFG D    G++ + G  V +  P  A+  G+A  PE+RK  G+  +++V  N  + 
Sbjct: 309 ARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENIVLA 368

Query: 362 VASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPK 421
           + +R    G+ R+R    +AR  +Q L +K A  ETPVG LSGGNQQKV+LARWL   P+
Sbjct: 369 LQARQGWRGMSRARQ-DELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVTEPR 427

Query: 422 VLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481
           +LILDEPTRG+D+ AK E+   V R A  G+AV+ IS+E  E+   CDR+ VMRE    G
Sbjct: 428 LLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRKAG 487

Query: 482 ELAGAAITQENIMRLATD 499
           EL G +     +  +A D
Sbjct: 488 ELPGGSTEARVLAMIAGD 505



 Score =  114 bits (284), Expect = 1e-29
 Identities = 81/272 (29%), Positives = 139/272 (51%), Gaps = 10/272 (3%)

Query: 253 IAPADAAQLPTVMQVRALA---GGKIRPASFDV--RAGEVLGFAGLVGAGRTELARLLFG 307
           + P   A  P V+Q R L    G  +     D+  RAGEV    G  GAG++ L +LL G
Sbjct: 1   MTPVSPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTG 60

Query: 308 ADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHT 367
            +    G + L+GR +    P  A R GI  V ++     L   ++VA N       R  
Sbjct: 61  VERPDRGSVELDGRVIAPSTPMEAQRDGIGTVYQE---VNLCPNLSVAENLYAGRYPRRR 117

Query: 368 RLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDE 427
           RL ++  R +   AR+ +++L++++   + P+G      +Q V +AR L ++ +VLILDE
Sbjct: 118 RLRMIDWRQVRDGARSLLRQLHLEL-DVDAPLGSYPVAIRQMVAIARALGVSARVLILDE 176

Query: 428 PTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAA 487
           PT  +D     E+++++ +L  +G+A++ ++  L +V  + DR+ V+R+G   GE A A 
Sbjct: 177 PTSSLDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVAD 236

Query: 488 ITQENIMRLATDTNVPRTAPA-SHSSPTPLAP 518
           +    ++      ++P  A A +  +P P AP
Sbjct: 237 LPPAALVNAMVGRDLPTVAGADAERAPPPDAP 268


Lambda     K      H
   0.320    0.135    0.378 

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: 764
Number of extensions: 40
Number of successful extensions: 8
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: 521
Length of database: 505
Length adjustment: 35
Effective length of query: 486
Effective length of database: 470
Effective search space:   228420
Effective search space used:   228420
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 (21.8 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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Protein sequences (fasta format)
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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
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