GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Thiothrix lacustris DSM 21227

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

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



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  266 bits (681), Expect = 5e-76
 Identities = 155/364 (42%), Positives = 215/364 (59%), Gaps = 27/364 (7%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           M+ LE++N+ K YG++  +K + + ++SGEF+V +G SGCGKSTLL +IAGL   +GG +
Sbjct: 1   MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
           ++  R +  V P  RD+AMVFQSYALYP+++V  N+ F L + +V  A   + V+  A  
Sbjct: 61  ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           L +   L R P  LSGGQRQRVAIGR++VR+P+VFLFDEPLSNLDA LR   R E+  LH
Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
           + L  T VYVTHDQ+EAMTLA R+ V+RDG IEQ+  P E+YD+P   +VA F+G P MN
Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240

Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300
           +                     PA+  G  +  +  +VGIRPE L++ +  E   L   V
Sbjct: 241 V--------------------APASLFG-QFPAQVAEVGIRPEHLQMVS-PEDGLLAGKV 278

Query: 301 EVVELTGPELVTTATVG----SQRITACLPPRTAVGMGSAHAFTFDGTA-LHLFDPESGR 355
            +VE  G E +           + +   L  RT V +G      +D +  +H FD +  R
Sbjct: 279 VLVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFDTKGMR 338

Query: 356 SLRM 359
              M
Sbjct: 339 LTHM 342


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: 336
Number of extensions: 8
Number of successful extensions: 1
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: 348
Length adjustment: 29
Effective length of query: 331
Effective length of database: 319
Effective search space:   105589
Effective search space used:   105589
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 Apr 09 2024. 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