GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gamP in Cronobacter universalis NCTC 9529

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC

Query= SwissProt::P39816
         (631 letters)



>NCBI__GCF_001277175.1:WP_038857764.1
          Length = 499

 Score =  371 bits (953), Expect = e-107
 Identities = 213/498 (42%), Positives = 306/498 (61%), Gaps = 42/498 (8%)

Query: 2   FKKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVG 61
           F K+   L  +GRALM P+++LPAAGLLL FGDK   ++P++ +AGGV+FDNLPL+FA+G
Sbjct: 7   FVKSLSKLSMIGRALMLPISLLPAAGLLLAFGDK--FHLPLMMNAGGVIFDNLPLLFAIG 64

Query: 62  VAIGLAGGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPY--EGAEHL-------IDMGV 112
            A+GLA   G+A L+A +   I+ +T+      LG+ P     G ++        + MGV
Sbjct: 65  SAVGLASESGIAALSAAVSVFIINITISTQ---LGITPEMAASGGKYAMVVGIPTLQMGV 121

Query: 113 FGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSFVWPLIQNG 172
           FGG+I G+LAA+ Y RF +++L   LGFFSGKRFV I  +  S ++G+   +VW  IQ G
Sbjct: 122 FGGLISGILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQAG 181

Query: 173 INAASSLIA--DSTVGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTGNTVTGDL 230
           I+A S ++   +     F +  + R LIP GLHHI+Y  F++  G+YT   TG  + GD 
Sbjct: 182 IDALSVIVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTT-QTGQVIHGDQ 240

Query: 231 TRFFA------------GDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVM 278
           T +F                 AG+FM G+FP M+F LPA  LA+ H A  + KK+ SG++
Sbjct: 241 TIWFKMLEEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGIL 300

Query: 279 ISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDY 338
            SAALT  LTGITEPVEF+F+FVAPVLY+ N+I+AG+ ++   L       +FS G IDY
Sbjct: 301 FSAALTCFLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLIDY 360

Query: 339 VLNYGL--STNGWV-----VIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEK 391
           + ++G+  S NG+       + VGI  A IYY+ FRF I ++++KTPGR  D     ++K
Sbjct: 361 I-SFGILPSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGR-VDVTASADDK 418

Query: 392 APVAKDQLAFHVLQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEV-N 450
                 +LA +++  LGG++NI ++ ACITRLR+ V +P  V KD L  LGA GV+ V +
Sbjct: 419 TDA---ELAGNIVGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGD 475

Query: 451 NNFQAIFGTKSDALKDDI 468
           N  Q IFG ++  +   +
Sbjct: 476 NGIQVIFGARAQFIAQSL 493


Lambda     K      H
   0.324    0.142    0.421 

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: 832
Number of extensions: 43
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: 631
Length of database: 499
Length adjustment: 36
Effective length of query: 595
Effective length of database: 463
Effective search space:   275485
Effective search space used:   275485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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