GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagPcb in Shewanella loihica PV-4

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__PV4:5210198
          Length = 490

 Score =  273 bits (698), Expect = 9e-78
 Identities = 167/464 (35%), Positives = 250/464 (53%), Gaps = 40/464 (8%)

Query: 4   FLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFV--------YQAGTAVFDHLPLIFA 55
           F Q+L ++ +LPIA+LPA G+++ L       IPF+        +  G  VF  +P++FA
Sbjct: 26  FAQRLSQALLLPIAILPAAGVMIGLATNP---IPFISADLATLMWTVGNLVFSMMPMLFA 82

Query: 56  IGIAIGISKDSNGAAGLSGAISYLMLDAATKTIDK-------------TNNMAVFGGIIA 102
           + IAIG  +D  G A  S    Y +  ++   + K             T +  + GG++ 
Sbjct: 83  VTIAIGFCRDQ-GIAAFSAVFGYGVFFSSLSALAKIYHLPTEMILGQATIDTGIAGGMMV 141

Query: 103 GLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGE 162
           G          +  +LP    FF GRR  P+L   + I+LA +F ++WP + + I     
Sbjct: 142 GAFTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISN 201

Query: 163 WMLGLGGIGA-GIFGLFNRLLIPLGLHHVLNNIFWFQFGEY-NG---VTGDLARFFAKDP 217
           W +      A  ++G+  RLLIPLGLHH+ N  F+ + G+Y NG   V G++AR+ A DP
Sbjct: 202 WAVYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGDEWVRGEVARYLAGDP 261

Query: 218 TAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAF 277
            AG    G+  I M+GLPAA LA+   A   +R   AG+M+  A   ++TG+TEPIEFAF
Sbjct: 262 QAGNLAGGYL-IKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAF 320

Query: 278 MFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICY 337
           MF++PLL+ +HA++TG++  +   L I     FS G +D+ L  G +      L++G   
Sbjct: 321 MFVAPLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSLLLGQSRNVEWFLILGPLT 380

Query: 338 AAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHC 397
           A +Y++VF   I A NLKTPGR        ++  + Q      M+  LGG++N+  +  C
Sbjct: 381 AVIYYLVFRGAILAFNLKTPGR--------MEAGSGQRAGLISMITALGGQDNINELTAC 432

Query: 398 ATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441
            TRLR++VK   LVD+A L K GAKGVV   G  VQ++ G   E
Sbjct: 433 LTRLRISVKHAELVDKAQLNKLGAKGVVLV-GNGVQLVYGTKAE 475


Lambda     K      H
   0.326    0.144    0.429 

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: 553
Number of extensions: 34
Number of successful extensions: 7
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: 452
Length of database: 490
Length adjustment: 33
Effective length of query: 419
Effective length of database: 457
Effective search space:   191483
Effective search space used:   191483
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 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