Alignments for a candidate for HSERO_RS03640 in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Moritella dasanensis ArB 0140

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_017221119.1 A923_RS0107850 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000276805.1:WP_017221119.1
          Length = 501

 Score =  410 bits (1054), Expect = e-119
 Identities = 216/505 (42%), Positives = 319/505 (63%), Gaps = 12/505 (2%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           MTQ  +L++ GI KSF    AL +  L + PG++ AL+GENGAGKSTLMKVL+G++  D+
Sbjct: 1   MTQA-ILKLSGIEKSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDK 59

Query: 61  GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAM 120
           G I   G  V    P  S+  GI++I+QEL + P +++A N+++G E     G I    M
Sbjct: 60  GSINYQGSDVTFDGPRHSQEVGISIIHQELNLIPELTIAENIYLGRETTNAFGGIKWTQM 119

Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
            +  DA+L++L     +  L G LS+ EQQ VEIA+AL  +S++++MDEPT AL+E ET+
Sbjct: 120 FADADALLQRLNVKHSSRQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETK 179

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            LF V+  LR+EG  I+YISHR+ E++ + D +TVLRDG F+ E+   +ID + +++ MV
Sbjct: 180 SLFKVINELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIEKMV 239

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300
           GR L E Y        DA      ++V  +    +R  SF +  GE+LG +GL+GAGRTE
Sbjct: 240 GRRLDEIYPR-----IDAKHGTLCLEVENIVAPGVRDVSFTLDHGEILGISGLMGAGRTE 294

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAAN--- 357
           L + ++GA PR  GD++L+ + V    PR  +  GIAY+ EDRKG GL L ++V  N   
Sbjct: 295 LMKAIYGALPRQSGDVILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSL 354

Query: 358 ATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLE 417
             ++  S+  +L   +  +        +++ NVK    +  +G LSGGNQQKV +A+ L 
Sbjct: 355 CALDALSKGLQLDHAKEAT---AVEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLM 411

Query: 418 IAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREG 477
             PKVLILDEPTRGVD+ AK EIYQL+++  ++G++++++SSE+PEV+G+ DR+LVM EG
Sbjct: 412 TRPKVLILDEPTRGVDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEG 471

Query: 478 MITGELAGAAITQENIMRLATDTNV 502
            I+GE   A   QE +M  A    +
Sbjct: 472 RISGEFMAADANQEKLMACAVGKKI 496



 Score =  111 bits (278), Expect = 5e-29
 Identities = 67/233 (28%), Positives = 124/233 (53%), Gaps = 15/233 (6%)

Query: 24  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83
           D+  T+  GEI  + G  GAG++ LMK + G      G+++LD + V+   P    A GI
Sbjct: 271 DVSFTLDHGEILGISGLMGAGRTELMKAIYGALPRQSGDVILDDKVVSPITPRDGLANGI 330

Query: 84  NLIYQE---------LAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQLGAG 134
             I ++         L+V  N+S+ A   +   L+     +DHA   +  +  +RQ    
Sbjct: 331 AYISEDRKGDGLILGLSVKENMSLCALDALSKGLQ-----LDHAKEATAVEDFMRQFNVK 385

Query: 135 FGASD-LAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEG 193
             + D + G LS   QQ+V IA+ L+ R +++I+DEPT  +     ++++ ++ + + EG
Sbjct: 386 TPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKAEG 445

Query: 194 LAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246
           ++II +S  M EV  ++DR+ V+ +G   GE +  + + E+++   VG+ ++E
Sbjct: 446 MSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADANQEKLMACAVGKKINE 498


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: 646
Number of extensions: 32
Number of successful extensions: 7
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: 501
Length adjustment: 35
Effective length of query: 486
Effective length of database: 466
Effective search space:   226476
Effective search space used:   226476
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 24 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
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