Alignments for a candidate for HSERO_RS03640 in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Rhodobacter viridis JA737

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_110805879.1 C8J30_RS10885 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_003217355.1:WP_110805879.1
          Length = 511

 Score =  349 bits (896), Expect = e-100
 Identities = 197/483 (40%), Positives = 292/483 (60%), Gaps = 13/483 (2%)

Query: 7   LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66
           L +RG  K +  T AL  +   +R G ++ L+GENGAGKSTLMK+++GV    +G I +D
Sbjct: 9   LSIRGGVKVYPGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDMTEGTITMD 68

Query: 67  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL-IDHAAMRSRTD 125
           GR +  R    + AAGI +++QEL + PN+SVA N+F+G E  TR G+ ID  A R  T 
Sbjct: 69  GREMRFRTKADAVAAGIGIVFQELNLFPNLSVAENIFIGHET-TRGGIDIDIEAHREATR 127

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            ++ +L          G L I +QQ VEIA+AL   +RI+I+DEPT+ALS  E E LF V
Sbjct: 128 QLMERLEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEVLFRV 187

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +  L  +G+ I+YISHR+ E+  + D +TVLRDG   G    + +D   IV+ M+G S  
Sbjct: 188 IDELTAQGVGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVDIPWIVKAMIGSSSK 247

Query: 246 EFYQHQ------RIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRT 299
           E+ + +       I  A+   LP     RA  G  +   S  +R+GE++G  GL+GAGR+
Sbjct: 248 EYGRSEVANFGPEIFRAEDITLP-----RAGGGFTVDHVSLSIRSGEIVGLYGLMGAGRS 302

Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 359
           E    +    P SGG   +EG+P+        +  GIA +PEDRK  GL   M++  N T
Sbjct: 303 EFLECVMAQHPHSGGKFWVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIRENLT 362

Query: 360 MNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419
           ++     T+L  +  +     A   I+RL +KVA PE PV  LSGGNQQKV++ + L   
Sbjct: 363 LSSLPSFTKLFHLDLKKEAKTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVIGKALMTG 422

Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479
           PKVL++DEP+RG+DI AK+E+++ + RLA++G+ ++ ++S+L EV+ + DR++VM +G +
Sbjct: 423 PKVLLMDEPSRGIDIGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMAQGRV 482

Query: 480 TGE 482
           TGE
Sbjct: 483 TGE 485



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 67/260 (25%), Positives = 115/260 (44%), Gaps = 27/260 (10%)

Query: 17  GATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPG 76
           G    +  + L+IR GEI  L G  GAG+S  ++ +   H    G+  ++G+P+  RD  
Sbjct: 273 GGGFTVDHVSLSIRSGEIVGLYGLMGAGRSEFLECVMAQHPHSGGKFWVEGKPLTERDVP 332

Query: 77  ASRAAGINLIYQEL---AVAPNISVAANVFMGS-ELRTRLGLIDHAAMRSRTDAVLRQLG 132
              A GI LI ++     +   +S+  N+ + S    T+L  +D           +++L 
Sbjct: 333 GRIARGIALIPEDRKRDGLIQIMSIRENLTLSSLPSFTKLFHLDLKKEAKTAVEFIKRLT 392

Query: 133 AGFGASDL-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRD 191
               + +     LS   QQ+V I +AL+   ++++MDEP+  +      ++F  +RRL  
Sbjct: 393 IKVASPENPVSSLSGGNQQKVVIGKALMTGPKVLLMDEPSRGIDIGAKAEVFRTMRRLAA 452

Query: 192 EGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSEFYQHQ 251
           EGL I++++  + EV AL+DR+ V                      M  GR   EF    
Sbjct: 453 EGLGILFVTSDLDEVLALSDRIIV----------------------MAQGRVTGEFPSGT 490

Query: 252 RIAPADAAQLPTVMQVRALA 271
             A   +A  P     + +A
Sbjct: 491 EAAKVISATTPNAQNSKDIA 510


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: 680
Number of extensions: 26
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: 521
Length of database: 511
Length adjustment: 35
Effective length of query: 486
Effective length of database: 476
Effective search space:   231336
Effective search space used:   231336
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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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 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