GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Marinobacter adhaerens HP15

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF4122 HP15_4062 spermidine/putrescine ABC transporter, ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Marino:GFF4122
          Length = 373

 Score =  234 bits (597), Expect = 3e-66
 Identities = 140/361 (38%), Positives = 213/361 (59%), Gaps = 34/361 (9%)

Query: 6   LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65
           L ++ K + G+T   +   +L+I D EF   +GPSGCGKTT LR++AG E   EG + + 
Sbjct: 8   LSNLSKQFGGKT--VLDGLDLEIYDGEFITLLGPSGCGKTTLLRLMAGFEHPDEGTITLA 65

Query: 66  DRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI 125
              +    P++R +  VFQ+YAL+PHM+V+ N+A+GLK+ K PK EI +RV EA  ++ +
Sbjct: 66  GENLTHTAPENRPLNTVFQHYALFPHMSVFDNVAYGLKMEKRPKDEIRQRVDEALAMVQL 125

Query: 126 AHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRL 185
                RKP  LSGGQ+QRVA+ RA+V+ P++ L+DEPLS LD KLR  M+ E+++L + L
Sbjct: 126 QDFARRKPHQLSGGQQQRVAIARAVVKRPRLLLLDEPLSALDYKLRRTMQVELKRLQREL 185

Query: 186 QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIR 245
             T ++VTHDQ EA++M DR+VV++DG++QQ  TP+ VY +P N+F A F+G    NF  
Sbjct: 186 GITFVFVTHDQEEALSMSDRVVVLKDGLVQQLGTPREVYERPANLFTARFVGE--TNFFP 243

Query: 246 G--EIVQDG----DAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299
           G  E VQDG    D F  +    +LR P+      ++   +       +RPED+   E  
Sbjct: 244 GTVESVQDGSIKVDVFGLKR---TLRRPDFPVQAEQSLHVL-------LRPEDIRVLE-- 291

Query: 300 MTTYPDSVLQMQVEVVE--HMGS--EVYLHTSIGPNTIVARV----NPRHVYHVGSSVKL 351
               PD    +  ++VE  + GS  +  +H + G   + +      +P   Y +G  VK+
Sbjct: 292 ----PDDENGVAGKIVERNYKGSTLDSVIHLADGTEVLASEFFDEDDPAFDYRLGEPVKV 347

Query: 352 A 352
           +
Sbjct: 348 S 348


Lambda     K      H
   0.321    0.138    0.395 

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: 370
Number of extensions: 16
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: 384
Length of database: 373
Length adjustment: 30
Effective length of query: 354
Effective length of database: 343
Effective search space:   121422
Effective search space used:   121422
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: 50 (23.9 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