GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__Dino:3608624
          Length = 333

 Score =  285 bits (729), Expect = 1e-81
 Identities = 157/309 (50%), Positives = 203/309 (65%), Gaps = 25/309 (8%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           M+ L + N++K +G+ + + G+ I +  GEF+V++G SGCGKSTLL ++AGL   S G++
Sbjct: 1   MATLTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEV 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
            I  R V  + P DRDIAMVFQ+YALYP++SV  N+ +GL++ +VP+AE    V   A+L
Sbjct: 61  RIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKL 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           LQ+E  L RKP +LSGGQRQRVA+GRA+VR P VFLFDEPLSNLDAKLR++MR E+K L 
Sbjct: 121 LQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQ 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
           + L  T +YVTHDQ+EAMTLA R+ VM  G  +Q+ AP EVY  P T +VAGF+GSPP N
Sbjct: 181 RELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPPTN 240

Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300
            L A+M   G            PA            +VGIRPE LR+A      RL A V
Sbjct: 241 FLPADMVRAG------------PAG----------QQVGIRPEHLRVAPQG---RLEAHV 275

Query: 301 EVVELTGPE 309
              E  G E
Sbjct: 276 AYAEALGAE 284


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: 315
Number of extensions: 9
Number of successful extensions: 2
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: 360
Length of database: 333
Length adjustment: 29
Effective length of query: 331
Effective length of database: 304
Effective search space:   100624
Effective search space used:   100624
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: 49 (23.5 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:

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