GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcb in Shewanella amazonensis SB2B

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= TCDB::Q9HXN4
         (570 letters)



>FitnessBrowser__SB2B:6936959
          Length = 485

 Score =  291 bits (745), Expect = 4e-83
 Identities = 178/470 (37%), Positives = 262/470 (55%), Gaps = 31/470 (6%)

Query: 10  QRLGRALMLPIAILPIAGLLLRLGDVDLLDIP-----LVHDAGKAIFANLALIFAIGIAV 64
           QRL + L++PIAILP AG+++ +    L  IP     L+   GK IF  + ++FAI +A+
Sbjct: 24  QRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAIAVAI 83

Query: 65  GFARDNNGTAGLAGAIGYLVMISVLKVI-------------DPGIDMGVLSGIISGLVAG 111
           GF RD  G A  + A GY V++S L                 P ID G+  G++ G +  
Sbjct: 84  GFCRDQ-GIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGGITC 142

Query: 112 ALYNRFKDVKLPEYLAFFGGRRFVPIATGISAVCLGLLFGVIWPPLQQGINGLGQLMLES 171
                 + ++LP   +FF GRR  P+      + L ++   IWPPL   I  L    +  
Sbjct: 143 VAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWAVYQ 202

Query: 172 GSFGAFAF-GVLNRLLIVTGLHHILNNLVWFVFGSFTDPETGRVVTGDLARYFAGDPKGG 230
               AF F G++ RLL+  GLHHI N   +   G +     G +V G++ARYFAGDP  G
Sbjct: 203 EPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYA--HDGEIVRGEMARYFAGDPSAG 260

Query: 231 QFMAGMFPVMMFGLPAACLAMYRNARPERRKLIGGLLLSMALTAFLTGVTEPVEFAFMFL 290
             +AG + + M+GLPAA LA++R A   +R  + G++LS A  ++LTGVTEP+EFAF+F+
Sbjct: 261 N-LAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFLFV 319

Query: 291 APLLYLLHALLTGLSMALTDLLDIRLGFTFSGGAIDLALGWGRSTHGWMLWPLGLLYAGI 350
           APLLYL HALLTGL+ ++  LLD+     FS G +D  L + +S++   +W LG L   I
Sbjct: 320 APLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTFVI 379

Query: 351 YYLVFDFCIRRFNLKTPGREDDASSESGDNAEAERAPAFIRALGGAANLEVVDACTTRLR 410
           YY++F   I  FNLKTPGR +       D  +     A + ALGG  N+  + AC TRLR
Sbjct: 380 YYILFRASILAFNLKTPGRFE------ADTGQKRNLIAIVSALGGGGNIADLSACLTRLR 433

Query: 411 LRLVDRNKASDAQLKALGAMAVVRPGKAGSLQVVVGPQADSIADEIRRAL 460
           + + D ++    +L +LGA  V+  G    +Q+V G +A+++   ++R L
Sbjct: 434 ISVADPSQVDRQRLMSLGAKGVIVVG--SGVQLVFGTKAETLRKLLQRYL 481



 Score = 47.8 bits (112), Expect = 1e-09
 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 496 AWLGALGGAGNLREVRDVALTRLRVSVADERKLATEQLRRLGGQGVSSLAGGICHILVGP 555
           A + ALGG GN+ ++    LTRLR+SVAD  ++  ++L  LG +GV  +  G+  ++ G 
Sbjct: 411 AIVSALGGGGNIADL-SACLTRLRISVADPSQVDRQRLMSLGAKGVIVVGSGV-QLVFGT 468

Query: 556 RAAALSQALQPLL 568
           +A  L + LQ  L
Sbjct: 469 KAETLRKLLQRYL 481


Lambda     K      H
   0.326    0.143    0.428 

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: 633
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 570
Length of database: 485
Length adjustment: 35
Effective length of query: 535
Effective length of database: 450
Effective search space:   240750
Effective search space used:   240750
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: 40 (21.6 bits)
S2: 52 (24.6 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