Alignments for a candidate for HSERO_RS05250 in Rhizobium freirei PRF 81

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Rhizobium freirei PRF 81

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_004127105.1 RHSP_RS28505 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_000359745.1:WP_004127105.1
          Length = 513

 Score =  475 bits (1223), Expect = e-138
 Identities = 255/511 (49%), Positives = 348/511 (68%), Gaps = 9/511 (1%)

Query: 9   TTGVAASSSSSVP----VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTL 64
           +T  A  +S  VP    +++   + K FPGVLALD+  F L  G VHALMGENGAGKSTL
Sbjct: 6   STMAAVRASGVVPNAAYLLSAEGIRKEFPGVLALDDVSFHLKRGTVHALMGENGAGKSTL 65

Query: 65  MKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREP 124
           MKIL+G+Y  D GD+ L G  + +  P  A   GI +IHQELNLM +++ A+NI+I REP
Sbjct: 66  MKILAGIYIPDQGDVRLKGVEIRLKSPLDALENGIAMIHQELNLMPYMTVAENIWIRREP 125

Query: 125 RKAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIM 184
           +   G F+D  E+ R+   +F R+ + +DP   V EL+VA +QMVEIAKA+S++S VLIM
Sbjct: 126 KNRFG-FVDHTEMRRKTEELFHRLNISIDPEIQVRELSVANRQMVEIAKAVSYNSDVLIM 184

Query: 185 DEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPM 244
           DEPT+AL   E+A LF+IIRDL+ QG+GIVYI+HKM+EL +IAD  SV RDGKYI T   
Sbjct: 185 DEPTSALTEREVAHLFQIIRDLRTQGIGIVYITHKMNELFEIADEFSVFRDGKYIGTHAS 244

Query: 245 QETSMDTIISMMVGRALDGEQRIPPD-TSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILG 303
            + + D II MMVGR +   Q  P +     + VL V+ L+      +VSF +R GEILG
Sbjct: 245 TDVTRDDIIRMMVGREIT--QMFPKEEVPIGETVLSVKDLSLDGVFSNVSFDVRAGEILG 302

Query: 304 FAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLA 363
            AGL+G+GR+ VA  IFG  P  +G I + G  A I SPADA+ H + +L+EDRK  G  
Sbjct: 303 VAGLVGSGRSNVAETIFGVTPASSGTIQLFGKAATISSPADAIRHRMAFLTEDRKDTGCL 362

Query: 364 VGMDVQANIALSSM-GRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQ 422
           + + V  N+ ++ +  +F R GF+ +  I +A +   ++L +KTP+++++   LSGGNQQ
Sbjct: 363 LILSVLENMQVAVLHDKFVRGGFVQEGPIEQACEEMAKKLRVKTPNLDERIENLSGGNQQ 422

Query: 423 KIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMS 482
           K +I +W+L +  IL  DEPTRGIDVGAK+EI++L+  +A  G A++MISSE+PEVL MS
Sbjct: 423 KALIGRWMLTNPRILILDEPTRGIDVGAKAEIHRLVTEMARNGVAVIMISSEMPEVLGMS 482

Query: 483 HRVLVMCEGRITGELARADATQEKIMQLATQ 513
            R++VM EGR+TG L RADATQ K+M+LA Q
Sbjct: 483 DRIMVMHEGRVTGFLDRADATQVKVMELAAQ 513



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 65/228 (28%), Positives = 116/228 (50%), Gaps = 5/228 (2%)

Query: 288 AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVA 347
           A+ DVSF L++G +    G  GAG++ + + + G    + G++ + G +  +KSP DA+ 
Sbjct: 38  ALDDVSFHLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGDVRLKGVEIRLKSPLDALE 97

Query: 348 HGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTP 407
           +GI  + ++     L   M V  NI +    +  R GF+D   +R   +    +L I   
Sbjct: 98  NGIAMIHQE---LNLMPYMTVAENIWIRREPK-NRFGFVDHTEMRRKTEELFHRLNISID 153

Query: 408 SVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKA 467
             E Q R LS  N+Q + IAK +  + D+L  DEPT  +     + +++++  L  QG  
Sbjct: 154 P-EIQVRELSVANRQMVEIAKAVSYNSDVLIMDEPTSALTEREVAHLFQIIRDLRTQGIG 212

Query: 468 IVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515
           IV I+ ++ E+  ++    V  +G+  G  A  D T++ I+++   RE
Sbjct: 213 IVYITHKMNELFEIADEFSVFRDGKYIGTHASTDVTRDDIIRMMVGRE 260


Lambda     K      H
   0.320    0.135    0.372 

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: 642
Number of extensions: 21
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: 520
Length of database: 513
Length adjustment: 35
Effective length of query: 485
Effective length of database: 478
Effective search space:   231830
Effective search space used:   231830
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