GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztB in Dinoroseobacter shibae DFL-12

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= CharProtDB::CH_011913
         (426 letters)



>lcl|FitnessBrowser__Dino:3606889 Dshi_0319 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 411

 Score =  415 bits (1066), Expect = e-120
 Identities = 226/425 (53%), Positives = 290/425 (68%), Gaps = 25/425 (5%)

Query: 4   ASDPPKAGFRLSMLIYDTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFL 63
           AS PP   F L MLI DTR+R  T Q + L+  +    WL++NA  NL A G+D NFSFL
Sbjct: 10  ASGPPNQPFNLGMLINDTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFL 69

Query: 64  WTRAGYDLAQTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWL 123
              A Y++ QTLIPY++ DTH RA   GLLNTLLV+ LGCI ATI G + GVLRLS+NWL
Sbjct: 70  GQPASYEIDQTLIPYTSTDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWL 129

Query: 124 VARIMTVYVETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDS 183
           VA++M+VYVE FRNIP+L+WI+++  ++++  P P+ FR        GE+  A+M  +DS
Sbjct: 130 VAKVMSVYVEIFRNIPVLIWIVIISAVMSQALPQPRAFR--------GEDATATMVLWDS 181

Query: 184 VAVTNRGTNLPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQE 243
           VA TNRG  +PAP ++   G+V       V++  L+I+ +       +RR+   AK +  
Sbjct: 182 VAFTNRGVYIPAPVWNPGSGIV-------VAVFVLSIIGIFV-----FRRY---AKNLLF 226

Query: 244 ATGTRPTTWWPSLLILFAPISALLYGLG--FHLDYPQITKFDFTGGFQMLHSFTALLIAL 301
            TG        SL I F P     + +G    LDYP++  F+F GG  +  +  AL  AL
Sbjct: 227 NTGKLLPVGRISLAIFFVPTLLAFFVMGRPIGLDYPELGGFNFRGGINIRGTLIALWFAL 286

Query: 302 TLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLN 361
            LYT AFIAE VRAGI A+S+GQTEAA ALG+RP R MSL+ILPQALRVI+PP+ISQ+LN
Sbjct: 287 ALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIILPQALRVIIPPVISQYLN 346

Query: 362 LTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSI 421
           LTKNSSLA A+ YMDL GTLGG+TLNQTGR  EC+LL+ML YL ISL+IS+LMNLYN ++
Sbjct: 347 LTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYLLISLSISALMNLYNNAV 406

Query: 422 KLKER 426
           KLKER
Sbjct: 407 KLKER 411


Lambda     K      H
   0.326    0.139    0.419 

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: 500
Number of extensions: 19
Number of successful extensions: 3
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: 426
Length of database: 411
Length adjustment: 32
Effective length of query: 394
Effective length of database: 379
Effective search space:   149326
Effective search space used:   149326
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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