GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagP in Alistipes indistinctus YIT 12060

Align N-acetylglucosamine porter, NagP (characterized)
to candidate WP_009133853.1 HMPREF9450_RS05320 sugar MFS transporter

Query= TCDB::Q8EBL0
         (435 letters)



>NCBI__GCF_000231275.1:WP_009133853.1
          Length = 445

 Score =  289 bits (739), Expect = 1e-82
 Identities = 157/443 (35%), Positives = 265/443 (59%), Gaps = 27/443 (6%)

Query: 8   QKSSFLPMAIVAALFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALP 67
           +K+S   MAI+  +FFI GF +W+N  L+PY K   +LN FQ+ LI+F+ Y A    A+P
Sbjct: 13  RKTSVAAMAILGLMFFIFGFTSWVNSILVPYFKIGCELNHFQSYLIVFALYSAYLIMAIP 72

Query: 68  SAWVIRKVGYKNGMALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNP 127
           S+ ++++VG+K G+  G     +  L+FIPAA  + + +FL    V+GAG  +LQ A NP
Sbjct: 73  SSAILKRVGFKRGIMYGFFCTALGALIFIPAAWWRSYPVFLAGSFVIGAGSAMLQAAANP 132

Query: 128 YVVRLGPEESAAARVSVMGILNKGAGVIAPLVFSALIL-----DSFKDRIGTTL----TQ 178
           YV  +GP  +   R+++MGI NK AG++APL+F+A++L     D F      TL      
Sbjct: 133 YVTMIGPINTTVKRMAIMGICNKFAGLVAPLIFAAVVLKVTDSDLFVQLESATLDPAARS 192

Query: 179 VQIDEMANGLVLPYLGMAVFIGILALAVKKSPLPELS----NEDEVADHTDKSQIKAALS 234
             +D + + +++PY   A F+ ++ + ++ S LPEL+    N+ EVA   +     +   
Sbjct: 193 AMLDSLVHRVMVPYAIFAAFLIVIGVFIRFSMLPELNLEEKNKQEVAPGGEGK--TSVFQ 250

Query: 235 HPNLALGVLALFVYVAVEVIAGDTIGTFALSLGIDHYGVMT--SYTMVCMVLGYILGILL 292
            P L LGV+A+F+++  +V+  DTI ++A ++G+D     T  SYT+  ++LG +LG+LL
Sbjct: 251 FPYLILGVVAMFLHIGTQVVTIDTIISYAQTMGMDLLEAKTFPSYTLSLVILGNVLGVLL 310

Query: 293 IPRVISQPTALMISAILGLLLTLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGL 352
           IP++ISQ     I   LG LL+LG+++G+           V F G     ++  +  +GL
Sbjct: 311 IPKIISQTRVFQICCTLGFLLSLGVVWGNTQ---------VDFLGHHANISIWFLVGIGL 361

Query: 353 ANAIVWPAVWPLALSGMGKLTSTGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVM 412
           AN++V+  +WPLA+ G+G+ T TGS++LIM + G A  P+ +G ++    + +   + ++
Sbjct: 362 ANSLVYGGIWPLAIRGLGRFTKTGSSMLIMALFGNAVVPLIYGYIADTASL-RIAYFWIL 420

Query: 413 LPCYLFILFYAVKGHKMRSWSAK 435
           LP + +++FYA  G+++ SWS +
Sbjct: 421 LPGFAYLMFYAFCGYRITSWSGR 443


Lambda     K      H
   0.326    0.141    0.414 

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: 643
Number of extensions: 46
Number of successful extensions: 6
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: 435
Length of database: 445
Length adjustment: 32
Effective length of query: 403
Effective length of database: 413
Effective search space:   166439
Effective search space used:   166439
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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