GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Bacteroides thetaiotaomicron VPI-5482

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  236 bits (603), Expect = 7e-67
 Identities = 137/360 (38%), Positives = 202/360 (56%), Gaps = 22/360 (6%)

Query: 6   LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65
           + H+ K +  +T   + D  L+++  EF   +GPSGCGKTT LR+IAG +  +EG + I 
Sbjct: 12  VSHVSKFFGDKT--ALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRIS 69

Query: 66  DRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI 125
            + +   PP  R +  VFQ YAL+PH+ VY N+AFGLKL+K PK  I ++V+ A K++ +
Sbjct: 70  GKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMVGM 129

Query: 126 AHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRL 185
                R   +LSGGQ+QRVA+ RAIV EP+V L+DEPL+ LD K+R  M+ E++++H+ L
Sbjct: 130 TDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSL 189

Query: 186 QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIR 245
             T +YVTHDQ EA+T+ D IVVM +G IQQ  TP  +Y++P N FVA FIG    N + 
Sbjct: 190 GITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNILN 247

Query: 246 GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPD 305
           G ++ D            +R     +  +        PV + +RPEDL+        +P 
Sbjct: 248 GTMIHDK----------LVRFCGTEFECVDEGFGENTPVDVVIRPEDLY-------IFPV 290

Query: 306 SVLQMQVEVVE-HMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAE 364
           S +     VV+  +   V+   ++        V   H + VG+ V L +    IHI   E
Sbjct: 291 SEMAQLTGVVQTSIFKGVHYEMTVLCGGYEFLVQDYHHFEVGAEVGLLVKPFDIHIMKKE 350


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: 433
Number of extensions: 21
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: 463
Length adjustment: 32
Effective length of query: 352
Effective length of database: 431
Effective search space:   151712
Effective search space used:   151712
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