GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pantoea rwandensis LMG 26275

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A166R419
         (517 letters)



>NCBI__GCF_002095475.1:WP_084931811.1
          Length = 504

 Score =  363 bits (932), Expect = e-105
 Identities = 202/476 (42%), Positives = 299/476 (62%), Gaps = 8/476 (1%)

Query: 24  LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGRDYRPGSRSQAEEL 83
           L G  L +  GEV AL GENGAGKSTL +++GG   P +G +  +G   +      A   
Sbjct: 21  LKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTVYDKGEAVQIKGPKAAMAR 80

Query: 84  GIRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEAMAQVGLDAIDPDTLV 143
           GI ++ QE+ L   L+VAEN+FL +LP+   W    +LR  A   + ++G + IDP   V
Sbjct: 81  GITLIHQEMALAQELTVAENIFLHDLPTFIAW---PKLRAKAANILRRLGFE-IDPAATV 136

Query: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVSIIYISH 203
           G+L + HQQ+VEIAR L  D  V++ DEPTA+L+ ++   L E I+ L++ GV+I+YISH
Sbjct: 137 GDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLEIISDLRSVGVAIVYISH 196

Query: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGEHI-DMGPRKIGAPAL 262
           RL+E+ R+A R+ +++DG  +  E       ++++ LMVGR + +   D     +G   L
Sbjct: 197 RLDEVFRIADRMTIMKDGQWIATESPQQTTLQEVIRLMVGRPVDQLFSDRATYGMGEEVL 256

Query: 263 TVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADTADSGTVALGASAQV 322
            V+ L    KVRDVSF VRAGE+ G+ GL+G+GRTE+ RLIFGAD  DSG + L    + 
Sbjct: 257 RVEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCDSGDIYL--HGKK 314

Query: 323 VSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGN-MPVISSGGFVNNGDEMSLA 381
           VS+RSP  AV  GIAL+ EDRK +G++L   I AN+ + N   V++  GF+++  E  + 
Sbjct: 315 VSLRSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVV 374

Query: 382 QRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCTVMLFDEPTRGIDVGAKFDIY 441
            +    MR++ +     VS LSGGNQQKVV+ +W      V++ DEPTRG+DVGAK +IY
Sbjct: 375 SKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGGQVIILDEPTRGVDVGAKREIY 434

Query: 442 ALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLAAA 497
            L+ EL +QG A+VV+SS+  EL  +C+R+ V+S G +    + D +++++LL+ A
Sbjct: 435 QLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSMA 490



 Score = 63.5 bits (153), Expect = 2e-14
 Identities = 55/234 (23%), Positives = 112/234 (47%), Gaps = 10/234 (4%)

Query: 15  IGKTYAQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRFQGRDYRP 74
           + K  A+  +  +  ++  GEV+ L G  G+G++ ++++I G     +G +   G+    
Sbjct: 258 VEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCDSGDIYLHGKKVSL 317

Query: 75  GSRSQAEELGIRMVMQE---LNLLPTLSVAENLFLDN---LPSHGGWISRKQLRKAAIEA 128
            S  QA + GI +V ++     ++  + +  N+ + N   + +  G+I   +  +   + 
Sbjct: 318 RSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVVSKL 377

Query: 129 MAQVGLDAIDPDTLVGELGIGHQQMVEIAR--NLIGDCHVLILDEPTAMLTAREVEMLFE 186
             Q+ L        V  L  G+QQ V +A+  NL G   V+ILDEPT  +       +++
Sbjct: 378 AQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGG--QVIILDEPTRGVDVGAKREIYQ 435

Query: 187 QITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTL 240
            I  L  +G++++ IS    EL  +  R+ V+ +G +       +Y+ E L+++
Sbjct: 436 LIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSM 489


Lambda     K      H
   0.319    0.137    0.384 

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: 607
Number of extensions: 35
Number of successful extensions: 9
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: 517
Length of database: 504
Length adjustment: 35
Effective length of query: 482
Effective length of database: 469
Effective search space:   226058
Effective search space used:   226058
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:

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:

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:

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:

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