Alignments for a candidate for HSERO_RS03640 in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Nocardioides dokdonensis FR1436

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_068105359.1 I601_RS01185 ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>NCBI__GCF_001653335.1:WP_068105359.1
          Length = 504

 Score =  305 bits (782), Expect = 2e-87
 Identities = 180/478 (37%), Positives = 276/478 (57%), Gaps = 4/478 (0%)

Query: 7   LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66
           L +R + K FG+ +A   + LT+  GEIH L+GENGAGKSTLM VL G++  D GEI+LD
Sbjct: 3   LALREVTKRFGSLVANDRISLTVEGGEIHCLLGENGAGKSTLMNVLYGLYRADGGEIVLD 62

Query: 67  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126
           G       PG + AAGI +++Q   + P  +VA NV +G+E     G +D  A R+R   
Sbjct: 63  GEVQHFTGPGDAIAAGIGMVHQHFMLVPVFTVAENVMLGNEQTGFAGSLDLEAARARVRE 122

Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186
           +  + G       + G L +  QQ+VEI + L   +++++ DEPTA L+ +ET++L  ++
Sbjct: 123 ISDRFGFHVDPDAVVGDLPVGVQQRVEIIKVLSRDAKVLVFDEPTAVLTPQETDELMEIM 182

Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246
           R LR  G AI++I+H++ EV  +ADR+TV+R G+ VGE      ++E +  MMVGR +  
Sbjct: 183 RELRRSGAAIVFITHKLREVREVADRITVIRRGTVVGEADPAASNAE-LAAMMVGRPVEL 241

Query: 247 FYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305
               Q       A +   + V   AG   +   SF+VRAGE+L  AG+ G G+TEL   L
Sbjct: 242 TVDKQDPELGGTALVVDGLSVFDSAGLVHVDDISFEVRAGEILAVAGVQGNGQTELTEAL 301

Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA-- 363
            G      G ILL+G+ +   + R  + AG+ +VPEDR+  GL     +A N  ++ +  
Sbjct: 302 LGLQDHVEGSILLDGQELVGRKVRDVLDAGVGFVPEDRQVDGLVGSFTIAENLMLDRSFD 361

Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423
           +   R G ++  +L   A   +++ +V+     TP G LSGGNQQKV++AR L    ++L
Sbjct: 362 APFVRHGSLQLSALQAFAEEKLEQYDVRAPGITTPAGNLSGGNQQKVVVARELSRELRLL 421

Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITG 481
           +  +PTRGVD+ +   I+Q +      GV V+V+S+EL EV+ + DR++V+  G I G
Sbjct: 422 VAAQPTRGVDVGSIEFIHQQIVATRDAGVPVLVVSTELDEVVALADRIMVLFRGRIVG 479



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 69/216 (31%), Positives = 105/216 (48%), Gaps = 11/216 (5%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           S  V  GE+    G  GAG++ L  +L+G     GG+I+L+G   H   P  A+ AGI  
Sbjct: 22  SLTVEGGEIHCLLGENGAGKSTLMNVLYGLYRADGGEIVLDGEVQHFTGPGDAIAAGIGM 81

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAH---P 395
           V +       F+ + V   A  NV   + + G   S  L   ARA ++ ++ +      P
Sbjct: 82  VHQH------FMLVPVFTVAE-NVMLGNEQTGFAGSLDLEA-ARARVREISDRFGFHVDP 133

Query: 396 ETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVV 455
           +  VG L  G QQ+V + + L    KVL+ DEPT  +      E+ +++  L   G A+V
Sbjct: 134 DAVVGDLPVGVQQRVEIIKVLSRDAKVLVFDEPTAVLTPQETDELMEIMRELRRSGAAIV 193

Query: 456 VISSELPEVIGICDRVLVMREGMITGELAGAAITQE 491
            I+ +L EV  + DR+ V+R G + GE   AA   E
Sbjct: 194 FITHKLREVREVADRITVIRRGTVVGEADPAASNAE 229



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 61/214 (28%), Positives = 104/214 (48%), Gaps = 7/214 (3%)

Query: 22  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 81
           + D+   +R GEI A+ G  G G++ L + L G+    +G ILLDG+ +  R       A
Sbjct: 271 VDDISFEVRAGEILAVAGVQGNGQTELTEALLGLQDHVEGSILLDGQELVGRKVRDVLDA 330

Query: 82  GINLIYQELAV---APNISVAANVFMGSELRT---RLGLIDHAAMRSRTDAVLRQLGAGF 135
           G+  + ++  V     + ++A N+ +         R G +  +A+++  +  L Q     
Sbjct: 331 GVGFVPEDRQVDGLVGSFTIAENLMLDRSFDAPFVRHGSLQLSALQAFAEEKLEQYDVRA 390

Query: 136 -GASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGL 194
            G +  AG LS   QQ+V +AR L    R+++  +PT  +     E +   +   RD G+
Sbjct: 391 PGITTPAGNLSGGNQQKVVVARELSRELRLLVAAQPTRGVDVGSIEFIHQQIVATRDAGV 450

Query: 195 AIIYISHRMAEVYALADRVTVLRDGSFVGELVRD 228
            ++ +S  + EV ALADR+ VL  G  VG +  D
Sbjct: 451 PVLVVSTELDEVVALADRIMVLFRGRIVGIVPAD 484


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: 728
Number of extensions: 30
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: 521
Length of database: 504
Length adjustment: 35
Effective length of query: 486
Effective length of database: 469
Effective search space:   227934
Effective search space used:   227934
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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Candidates (tab-delimited)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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