GapMind for catabolism of small carbon sources

 

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

Align N-acetylglucosamine porter, NagP (characterized)
to candidate 353837 BT4311 glucose/galactose transporter (NCBI ptt file)

Query= TCDB::Q8EBL0
         (435 letters)



>FitnessBrowser__Btheta:353837
          Length = 386

 Score =  246 bits (627), Expect = 1e-69
 Identities = 153/418 (36%), Positives = 238/418 (56%), Gaps = 40/418 (9%)

Query: 21  LFFILGFATWLNGSLMPYLKQILQLNPFQASLILFSFYIAVTFTALPSAWVIRKVGYKNG 80
           +FF LGFA  +N  L+P LK  L+++  ++ LI+ + +I       P+   I+K+GYK  
Sbjct: 1   MFFSLGFALGINSVLVPVLKGSLEISSAESYLIIAATFIPFLIFGYPAGLTIKKIGYKRT 60

Query: 81  MALGMGVMMIAGLLFIPAAKTQVFALFLFAQLVMGAGQTLLQTAVNPYVVRLGPEESAAA 140
           M L   +  IA  LFIP+A  + F LFL A  + G+    LQ AVNPY+  LGP +SAA 
Sbjct: 61  MVLSFLMFAIAFGLFIPSASYESFPLFLLASFISGSANAYLQAAVNPYITILGPIDSAAK 120

Query: 141 RVSVMGILNKGAGVIAPLVFSALILDSFKDRIGTTLTQVQIDEMANGLVLP-YLGMAVFI 199
           R+S+MGI NK A  I PL  + L        IG  +T + + +    L LP Y+ +A FI
Sbjct: 121 RISIMGICNKLAWPIPPLFLAFL--------IGKEVTDITVAD----LFLPFYVIIAAFI 168

Query: 200 GILALAVKKSPLPEL-----SNEDEVADHTDKSQIKAAL-SHPNLALGVLALFVYVAVEV 253
             L +    +PLPE+      + +E A+    +  K ++   P+L LG LALF+YV VE 
Sbjct: 169 A-LGIIAYMAPLPEVKAVGEDDSEEAAEACPYAAKKTSIWQFPHLLLGCLALFLYVGVET 227

Query: 254 IAGDTIGTFALSLGIDHYGVMTSYTMVCMVLGYILGILLIPRVISQPTALMISAILGLLL 313
           ++  T+  +A SL +++  +      + +V+GYI GI+ IP+ +SQ TAL I ++L +  
Sbjct: 228 VSLGTLVDYATSLHLENAAMYAWIAPIGIVIGYICGIIFIPKYMSQATALKICSVLAI-- 285

Query: 314 TLGILFGDNNSYAIANLLLVPFGGVALPDTLLLIAFLGLANAIVWPAVWPLALSGMGKLT 373
                        I ++L+V         ++  I+F+ L  +++WPA+WPLA++ +GK T
Sbjct: 286 -------------IGSVLVVL---TPADISIYFISFMALGCSLMWPALWPLAMADLGKFT 329

Query: 374 STGSALLIMGIAGGAFGPVSWGLMSSATDMGQQGGYMVMLPCYLFILFYAVKGHKMRS 431
            +GS+LLIM +AGGA  P  +G +   +D+  Q  Y + LPC+LFIL+Y V G+K+R+
Sbjct: 330 KSGSSLLIMAMAGGAVIPTLFGYLKDISDI--QKAYWICLPCFLFILYYGVAGYKIRT 385


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: 524
Number of extensions: 29
Number of successful extensions: 4
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: 386
Length adjustment: 31
Effective length of query: 404
Effective length of database: 355
Effective search space:   143420
Effective search space used:   143420
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: 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