GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Pantoea rwandensis LMG 26275

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_084931762.1 HA51_RS02835 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_002095475.1:WP_084931762.1
          Length = 500

 Score =  380 bits (976), Expect = e-110
 Identities = 216/495 (43%), Positives = 323/495 (65%), Gaps = 12/495 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L    I K +    AL  V F V  G+VH L+GENGAGKSTLL IL G    DSG + ++
Sbjct: 6   LMMRGITKTYGSAIALQDVDFMVRPGEVHALIGENGAGKSTLLNILSGVRPADSGAIHVN 65

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLG--WVNKREAKRFVR 122
           G +V+  +  S+  AGIA+IHQELQ+VP+L+VA+N+ LG+   +L   +V+KR       
Sbjct: 66  GEQVQMKNPLSARHAGIAMIHQELQHVPELSVAQNMFLGRPLTTLNGLFVDKRAQLARAT 125

Query: 123 ERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKL 182
             L+ +  +++P   ++ L ++Q+Q+VEI +ALL  A++IA+DEPTSSL+ RE E L +L
Sbjct: 126 HILKQLDPSINPAEPIKNLKVSQQQIVEIARALLDEAKIIAMDEPTSSLTPREFERLAEL 185

Query: 183 VRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREI 242
           + DL++   ++IY+SH+M+EI+++CD  TI RDGR++     +   T +TIV++MVGR+I
Sbjct: 186 IADLKSTGVSLIYVSHKMNEIFQVCDRATIMRDGRQVGV-VNICDETEETIVAKMVGRKI 244

Query: 243 SDIYNYS---ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299
               + S    R + +V   A+G E     +PASF V  GE++G  GLVGAGR+EL+ L+
Sbjct: 245 DKQAHQSWATDRKVLQVENVARGTE----IKPASFSVCAGEVLGVAGLVGAGRTELLKLI 300

Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359
            G D +  GE+ ++G+ ++  +   AIR GI L PEDRK+EGI+    V  N+ +   R+
Sbjct: 301 AGIDKRSAGEVRVNGQLVRNHNVSAAIRAGIGLVPEDRKKEGIIKARAVKVNMALPSMRN 360

Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419
           +   G+    K  A  A   +  LK++  +  + I  LSGGNQQK I+ RW+A  D +V 
Sbjct: 361 FTLAGVIRKVKLNA-VAQEVMSDLKLRPLNIEKPIGTLSGGNQQKVIIGRWVA-ADAEVF 418

Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479
           + DEPTRGID+GAK EIYN+I +LA++G AIV++SSE+ E+L VSDR++VMR+G+I+ EL
Sbjct: 419 LFDEPTRGIDIGAKAEIYNLIEKLAQQGKAIVVVSSEMTEILRVSDRVLVMREGKITREL 478

Query: 480 TRKDATEQSVLSLAL 494
           T  D TE+++   A+
Sbjct: 479 TGDDITEENIARFAI 493


Lambda     K      H
   0.320    0.136    0.385 

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: 648
Number of extensions: 37
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 512
Length of database: 500
Length adjustment: 34
Effective length of query: 478
Effective length of database: 466
Effective search space:   222748
Effective search space used:   222748
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