GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6936959 Sama_1133 PTS system,
           glucose-specific IIBC component (RefSeq)
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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