GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Desulfacinum infernum DSM 9756

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

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



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  333 bits (854), Expect = 4e-96
 Identities = 186/367 (50%), Positives = 246/367 (67%), Gaps = 12/367 (3%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           M+ +++  + KR+ +   ++   + +   EF+VL+G SGCGKST L +IAGL E + G+I
Sbjct: 1   MAEIKLDQVNKRFKKNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSGEI 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
            IG R V  V PKDRDIAMVFQSYALYP+++V +N+ FGL  R VP+ E D+ V+  A +
Sbjct: 61  SIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAAEI 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           L I +LL R+P+QLSGGQRQRVA+GRA+VR+PQ FLFDEPLSNLDAKLR++MR EL +LH
Sbjct: 121 LGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAKLH 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
           + L++T+VYVTHDQIEAMTLA RI VM+DG+I Q+  P EVY+RPA  +VAGF+GSP MN
Sbjct: 181 ERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVAGFIGSPSMN 240

Query: 241 ILDAEMT--ANGLKIEGCEEVLPLP----AAFNGAAWAGRRVKVGIRPEALRLAAGSE-- 292
            LD  +   A  L ++G    L +P     AF G     R V  GIRPE ++   G    
Sbjct: 241 FLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRG--HVNRPVIFGIRPEDVKERPGDALP 298

Query: 293 --AQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFD 350
              + L A V+V E  G E++ TATVGS   TA + P  AV +        +   +HLFD
Sbjct: 299 EGVEPLRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPIDLAVNMNKMHLFD 358

Query: 351 PESGRSL 357
           PES ++L
Sbjct: 359 PESEQAL 365


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: 356
Number of extensions: 10
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: 368
Length adjustment: 29
Effective length of query: 331
Effective length of database: 339
Effective search space:   112209
Effective search space used:   112209
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