Alignments for a candidate for H281DRAFT_01113 in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Rhizobium leguminosarum 3841

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_011654712.1 RL_RS25580 sugar ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>NCBI__GCF_000009265.1:WP_011654712.1
          Length = 494

 Score =  391 bits (1005), Expect = e-113
 Identities = 215/492 (43%), Positives = 311/492 (63%), Gaps = 11/492 (2%)

Query: 15  FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEG-QLV 73
           FLE+  V K F GV ALR V LS + G+++ L+GENG GKSTLIKII+G Q PD G  +V
Sbjct: 4   FLELTHVSKHFGGVRALRDVDLSLEAGEVHCLVGENGSGKSTLIKIIAGVQAPDPGGSIV 63

Query: 74  IEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVL 133
           +EG  HARL  + +  +GI+ +YQDLSL PNMSVAEN+A+ S +      L R  +   +
Sbjct: 64  LEGREHARLDPILSTKSGIQVIYQDLSLFPNMSVAENIAIGSHMG-----LPRLANWNRI 118

Query: 134 AATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQK 193
              AA+A+  + +  + E   T++  L +A RQLVAI RA+A++AK VIMDEPT SLT+ 
Sbjct: 119 NDIAAKAMARINVNLDLE---TMVSDLSIANRQLVAICRAMAADAKLVIMDEPTASLTRH 175

Query: 194 EVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISE 253
           EVD+L+ V+ +L+++ +  +FVSH+LDE   I   V VLRDG K+     +E T  ++  
Sbjct: 176 EVDSLLRVVNDLKSRDICTVFVSHRLDEVMEIAERVTVLRDGGKVGTFDASEITSRRLET 235

Query: 254 LMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNEL 313
           LMTG        R    A ++VL VR  +R G + D+SF +  GEI+G+TGLL SGR EL
Sbjct: 236 LMTGHEFHYAPPRPGGEAAEVVLAVRNLSRPGHYEDISFDIRKGEIVGLTGLLGSGRTEL 295

Query: 314 ARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA 373
           A ++ G+ P   G + + G+ +   +   A    + YVPEDRL  GL L +PI  N++  
Sbjct: 296 ALSIFGMNPPSRGTIEVSGKPLIASSNRVAIASGVAYVPEDRLMLGLALGQPISANILAT 355

Query: 374 MISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDP 433
           ++ SL  +FG I+  +  A A+  +  L      ++ PV +LSGGNQQRV++G+W+A  P
Sbjct: 356 VLDSLAGKFGLINPAKRVAAADDWIVRLNTKVSDLENPVGTLSGGNQQRVVLGKWMATKP 415

Query: 434 RVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493
           RVLIL  PTVGVD+ +KD IY I+ RL+  G+G++LISD+  E+  +  R+L+M++G + 
Sbjct: 416 RVLILDSPTVGVDIKAKDGIYEIVHRLAAEGVGVLLISDEAQEVFYHTHRVLVMRQGRLV 475

Query: 494 AEYRADELSEAD 505
           +E   D LS  +
Sbjct: 476 SE--VDPLSSTE 485



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 58/221 (26%), Positives = 106/221 (47%), Gaps = 12/221 (5%)

Query: 289 DVSFKLHGGEILGVTGLLDSGRNELARALAGV-APAQSGDVLLDGQQIALRTPSDAKRHR 347
           DV   L  GE+  + G   SG++ L + +AGV AP   G ++L+G++ A   P  + +  
Sbjct: 22  DVDLSLEAGEVHCLVGENGSGKSTLIKIIAGVQAPDPGGSIVLEGREHARLDPILSTKSG 81

Query: 348 IGYVPEDRLNEGLFLDKPIRDNVITAMISSLRD--RFGQIDRTRAQALAEQTVKELQIAT 405
           I  + +D     LF +  + +N+       L     + +I+   A+A+A   V  L + T
Sbjct: 82  IQVIYQDL---SLFPNMSVAENIAIGSHMGLPRLANWNRINDIAAKAMARINVN-LDLET 137

Query: 406 PGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGI 465
                 V  LS  N+Q V I R +A D +++I+  PT  +     D + R++  L  R I
Sbjct: 138 M-----VSDLSIANRQLVAICRAMAADAKLVIMDEPTASLTRHEVDSLLRVVNDLKSRDI 192

Query: 466 GIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEADL 506
             + +S  L E+++  +R+ +++ G     + A E++   L
Sbjct: 193 CTVFVSHRLDEVMEIAERVTVLRDGGKVGTFDASEITSRRL 233



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 59/224 (26%), Positives = 101/224 (45%), Gaps = 9/224 (4%)

Query: 34  VSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIE 93
           +S   ++G+I  L G  G G++ L   I G  PP  G + + G P    S   A+A+G+ 
Sbjct: 272 ISFDIRKGEIVGLTGLLGSGRTELALSIFGMNPPSRGTIEVSGKPLIASSNRVAIASGVA 331

Query: 94  TVYQD---LSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALE-AVGLPGN 149
            V +D   L L     ++ N+     LAT    LA  F     A   A A +  V L   
Sbjct: 332 YVPEDRLMLGLALGQPISANI-----LATVLDSLAGKFGLINPAKRVAAADDWIVRLNTK 386

Query: 150 SEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQG 209
                  +  L    +Q V + + +A++ + +I+D PT  +  K  D +  ++  L A+G
Sbjct: 387 VSDLENPVGTLSGGNQQRVVLGKWMATKPRVLILDSPTVGVDIKAKDGIYEIVHRLAAEG 446

Query: 210 VTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISE 253
           V VL +S +  E +     V+V+R G+ +++      T+  + E
Sbjct: 447 VGVLLISDEAQEVFYHTHRVLVMRQGRLVSEVDPLSSTERNLQE 490


Lambda     K      H
   0.319    0.135    0.376 

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: 584
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 494
Length adjustment: 34
Effective length of query: 481
Effective length of database: 460
Effective search space:   221260
Effective search space used:   221260
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 (21.7 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