Alignments for a candidate for H281DRAFT_01113 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Herbaspirillum seropedicae SmR1

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

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



>FitnessBrowser__HerbieS:HSERO_RS03640
          Length = 502

 Score =  334 bits (857), Expect = 4e-96
 Identities = 186/498 (37%), Positives = 294/498 (59%), Gaps = 14/498 (2%)

Query: 14  PFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLV 73
           P L++ G+ K F    AL  + L+ + G+I+ L+GENG GKSTL+K++SG   PD+G+++
Sbjct: 9   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 68

Query: 74  IEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVL 133
           ++G P A      + AAGI  +YQ+L++ PN+SVA NV + SEL T  G +    D   +
Sbjct: 69  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLI----DHAAM 124

Query: 134 AATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQK 193
            +     L  +G    +   S L  +L +A +Q V IARA+   ++ VIMDEPT +L+++
Sbjct: 125 RSRTDAVLRQLGAGFGA---SDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSER 181

Query: 194 EVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISE 253
           E + L  V+  LR +G+ ++++SH++ E YA+   V VLRDG  + +    E    +I +
Sbjct: 182 ETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQ 241

Query: 254 LMTGRHLS----NERYRESAHAQ-DIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDS 308
           +M GR LS    ++R   +  AQ   V+ VR     G+    SF +  GE+LG  GL+ +
Sbjct: 242 MMVGRSLSEFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGA 300

Query: 309 GRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRD 368
           GR ELAR L G  P   GD+LL+G+ + +  P  A R  I YVPEDR  +GLFL   +  
Sbjct: 301 GRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAA 360

Query: 369 NVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRW 428
           N  T  ++S   R G +       +A   ++ L +     + PV  LSGGNQQ+VL+ RW
Sbjct: 361 NA-TMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARW 419

Query: 429 LAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMK 488
           L I P+VLIL  PT GVD+ +K  IY+++ RL+ +G+ +++IS +LPE++  CDR+L+M+
Sbjct: 420 LEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMR 479

Query: 489 KGHVSAEYRADELSEADL 506
           +G ++ E     +++ ++
Sbjct: 480 EGMITGELAGAAITQENI 497



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 64/251 (25%), Positives = 116/251 (46%), Gaps = 18/251 (7%)

Query: 272 QDIVLDVRGFTRAG----QFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGD 327
           Q  +L +RG  ++       SD+   +  GEI  + G   +G++ L + L+GV     G+
Sbjct: 7   QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 66

Query: 328 VLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA----MISSLRDRFG 383
           +LLDG+ +ALR P  ++   I  +         + +  +  N+  A    M S LR R G
Sbjct: 67  ILLDGRPVALRDPGASRAAGINLI---------YQELAVAPNISVAANVFMGSELRTRLG 117

Query: 384 QIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTV 443
            ID    ++  +  +++L  A  G       LS   QQ+V I R L    R++I+  PT 
Sbjct: 118 LIDHAAMRSRTDAVLRQLG-AGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTA 176

Query: 444 GVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSE 503
            +     + ++ +++RL   G+ II IS  + E+    DR+ +++ G    E   DE+  
Sbjct: 177 ALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS 236

Query: 504 ADLYHALLSEA 514
             +   ++  +
Sbjct: 237 ERIVQMMVGRS 247



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 63/229 (27%), Positives = 104/229 (45%), Gaps = 8/229 (3%)

Query: 31  LRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAA 90
           +R  S   + G++    G  G G++ L +++ GA P   G +++EG P        A+ A
Sbjct: 279 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 338

Query: 91  GIETVYQDLS---LLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLP 147
           GI  V +D     L   M+VA N   T  +A+   RL     R  L   A  A++ + + 
Sbjct: 339 GIAYVPEDRKGQGLFLQMAVAANA--TMNVASRHTRLGLVRSRS-LGGVARAAIQRLNV- 394

Query: 148 GNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRA 207
                  T + +L    +Q V +AR +    K +I+DEPT  +       +  ++  L +
Sbjct: 395 -KVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLAS 453

Query: 208 QGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMT 256
           QGV V+ +S +L E   I   V+V+R+G    +   A  T+  I  L T
Sbjct: 454 QGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLAT 502


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: 652
Number of extensions: 24
Number of successful extensions: 8
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: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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 17 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