Alignments for a candidate for HSERO_RS03640 in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Bradyrhizobium sp. BTAi1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_012046544.1 BBTA_RS31430 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_000015165.1:WP_012046544.1
          Length = 507

 Score =  498 bits (1281), Expect = e-145
 Identities = 275/501 (54%), Positives = 349/501 (69%), Gaps = 7/501 (1%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG-EI 63
           P+L+MRG+ KSF    AL  + LT+  GE+HALMGENGAGKSTLMK+LSG + PD G EI
Sbjct: 4   PILEMRGVSKSFFGIKALQKVDLTVYAGEVHALMGENGAGKSTLMKILSGAYRPDPGGEI 63

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
            +DG PV +  P   RAAGI++IYQEL++APN++VA N+++G E+ ++ GL+   AMR  
Sbjct: 64  RIDGHPVRIEGPLGGRAAGISIIYQELSLAPNLTVAENIYLGREV-SQSGLLARGAMREG 122

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
              +L +LGA F AS L   LS+ ++Q VEIARAL  RS+I+IMDEPT +LS  E+E+LF
Sbjct: 123 VGPILTRLGADFAASTLVAELSMGQRQLVEIARALHARSKILIMDEPTTSLSAGESEKLF 182

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
            ++R+LR EGLAIIYISHRM EVYAL DRVTVLRDG  VG L + EI ++ IV+MMVGR 
Sbjct: 183 ALIRQLRAEGLAIIYISHRMDEVYALGDRVTVLRDGRLVGSLDKPEIRADSIVRMMVGRD 242

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           +S FY+     P      P +  V    G +++  S  V AGEV+G AGL+GAGRTELA 
Sbjct: 243 VSSFYKKDH-DPHAKRDRPVLTAVDLGDGHRVKGCSLTVHAGEVVGLAGLIGAGRTELAH 301

Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363
           L+ GA P+  G + L+G  + I+ PR A+ AGIAY+ EDRK  GLFL M+ A N  + V 
Sbjct: 302 LIIGATPKMTGHVTLDGERIEIETPRDALDAGIAYLTEDRKALGLFLDMSCADNINLAVI 361

Query: 364 SRHTRLGLVRSRSLGGV-ARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
            R  RLG V  R    + A  A   L ++  +P   VG LSGGNQQKVLL+R L  APKV
Sbjct: 362 GRDARLGGVLDRDKARLRADEAFSALGIRAPNPGVTVGGLSGGNQQKVLLSRLLATAPKV 421

Query: 423 LILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGE 482
           LILDEPTRGVD+ AKSEIY ++  LA  G A++VISS+LPE++GICDRVLVMR G + GE
Sbjct: 422 LILDEPTRGVDVGAKSEIYSIIDNLAKSGTAILVISSDLPEILGICDRVLVMRCGQLAGE 481

Query: 483 LAGAA---ITQENIMRLATDT 500
           L  +A   ITQE+IM LAT T
Sbjct: 482 LQQSATTPITQEDIMALATGT 502



 Score =  106 bits (264), Expect = 2e-27
 Identities = 76/237 (32%), Positives = 126/237 (53%), Gaps = 23/237 (9%)

Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGA-DPRSGGDILLEGRPVHIDQPRAAMR 333
           ++     V AGEV    G  GAG++ L ++L GA  P  GG+I ++G PV I+ P     
Sbjct: 21  LQKVDLTVYAGEVHALMGENGAGKSTLMKILSGAYRPDPGGEIRIDGHPVRIEGPLGGRA 80

Query: 334 AGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQ------- 386
           AGI+ +         + ++++A N T+   + +  LG   S+S G +AR A++       
Sbjct: 81  AGISII---------YQELSLAPNLTV---AENIYLGREVSQS-GLLARGAMREGVGPIL 127

Query: 387 -RLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVH 445
            RL    A   T V +LS G +Q V +AR L    K+LI+DEPT  +      +++ L+ 
Sbjct: 128 TRLGADFA-ASTLVAELSMGQRQLVEIARALHARSKILIMDEPTTSLSAGESEKLFALIR 186

Query: 446 RLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNV 502
           +L ++G+A++ IS  + EV  + DRV V+R+G + G L    I  ++I+R+    +V
Sbjct: 187 QLRAEGLAIIYISHRMDEVYALGDRVTVLRDGRLVGSLDKPEIRADSIVRMMVGRDV 243


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: 784
Number of extensions: 35
Number of successful extensions: 11
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: 507
Length adjustment: 35
Effective length of query: 486
Effective length of database: 472
Effective search space:   229392
Effective search space used:   229392
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 Apr 09 2024. 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