Alignments for a candidate for HSERO_RS03640 in Succinatimonas hippei YIT 12066

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Succinatimonas hippei YIT 12066

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_009144323.1 HMPREF9444_RS09995 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000188195.1:WP_009144323.1
          Length = 498

 Score =  397 bits (1021), Expect = e-115
 Identities = 210/496 (42%), Positives = 318/496 (64%), Gaps = 7/496 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL+++GI KSF    AL ++ LT+  GEIHAL+GENGAGKSTLMK+L G+++ D+G+I +
Sbjct: 4   LLELQGISKSFPGVKALDNISLTLDKGEIHALLGENGAGKSTLMKILCGIYSNDEGKIFV 63

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
           +G+ V   +   +  AGI +I+QEL++ P ++   N+F+  E++   GLID A MR  T 
Sbjct: 64  EGKEVKFGNYKDAIDAGIGIIFQELSLIPYLNAVENIFLNREIKNAFGLIDFAKMRVETL 123

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            +L +L           +LS+AEQQ VEI +AL   ++I+++DEPT+ L+ +E + LF++
Sbjct: 124 KILDRLDVHINVDVPVEQLSVAEQQFVEIVKALSLNAKILVLDEPTSTLTPKEADHLFDI 183

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R L+ +G+ + +ISH + E++ + D ++VLRDG++VG     + + + +V+MMVGR + 
Sbjct: 184 MRELKQKGVGMFFISHHLDEIFEICDTISVLRDGTYVGTKPVKDSNVDELVEMMVGRKVE 243

Query: 246 EFYQHQ-RIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARL 304
             Y  +  + P +   L     +R   G   +P+SF +  GE+LGF GLVGAGRTE AR 
Sbjct: 244 NNYPPKPEVPPHEKVILEVNNLIREKHG---KPSSFKLYKGEILGFFGLVGAGRTETARA 300

Query: 305 LFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVAS 364
           L GADP    +++L+G+   +  P  A++ GI  +PEDRK +GL L  ++  N  MN  S
Sbjct: 301 LIGADPVYSKEVILDGKKETLGSPDVALQKGIGLLPEDRKAEGLILPFSITENIAMNNYS 360

Query: 365 RHTRLG--LVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
           +   +G   +  +     A+  I+++ VK    ET V  LSGGNQQKV++ RWL    KV
Sbjct: 361 KWI-VGKIFIDDKKEVETAKDLIKKVRVKTPSHETAVQNLSGGNQQKVVIGRWLNNDCKV 419

Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482
           LI DEPTRG+D+ AK+EIY+L+ +L  QG+++++ISSELPE+IG+CDRV V REG I  +
Sbjct: 420 LIFDEPTRGIDVGAKAEIYELMRKLTEQGISIIMISSELPEIIGVCDRVEVFREGAIVAD 479

Query: 483 LAGAAITQENIMRLAT 498
           L G  I    IM  AT
Sbjct: 480 LTGEDINSNTIMLYAT 495



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 59/216 (27%), Positives = 104/216 (48%), Gaps = 6/216 (2%)

Query: 32  GEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGINLIYQELA 91
           GEI    G  GAG++   + L G       E++LDG+   L  P  +   GI L+ ++  
Sbjct: 281 GEILGFFGLVGAGRTETARALIGADPVYSKEVILDGKKETLGSPDVALQKGIGLLPEDRK 340

Query: 92  VAPNI---SVAANVFMGSELRTRLGLI---DHAAMRSRTDAVLRQLGAGFGASDLAGRLS 145
               I   S+  N+ M +  +  +G I   D   + +  D + +              LS
Sbjct: 341 AEGLILPFSITENIAMNNYSKWIVGKIFIDDKKEVETAKDLIKKVRVKTPSHETAVQNLS 400

Query: 146 IAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRMAE 205
              QQ+V I R L +  +++I DEPT  +      +++ ++R+L ++G++II IS  + E
Sbjct: 401 GGNQQKVVIGRWLNNDCKVLIFDEPTRGIDVGAKAEIYELMRKLTEQGISIIMISSELPE 460

Query: 206 VYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
           +  + DRV V R+G+ V +L  ++I+S  I+    G
Sbjct: 461 IIGVCDRVEVFREGAIVADLTGEDINSNTIMLYATG 496


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: 598
Number of extensions: 29
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: 498
Length adjustment: 34
Effective length of query: 487
Effective length of database: 464
Effective search space:   225968
Effective search space used:   225968
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 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