Aligments for a candidate for nagF in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for nagF 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 6937494 Sama_1650 phosphotransferase system, enzyme I (RefSeq)

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__SB2B:6937494
          Length = 567

 Score =  299 bits (766), Expect = 3e-85
 Identities = 202/569 (35%), Positives = 294/569 (51%), Gaps = 21/569 (3%)

Query: 285 GVCASPGLASGPLARLGAISLPADDGR---HRPEEQHLALDQALQRVRDDVQGSLQQARL 341
           G+   PG+  G          P D       R  +Q   LD  L R++  +  SLQ   L
Sbjct: 5   GIAIKPGVTFGEALHFNTGHKPLDYRILPIKRIPQQLSRLDGGLARLKQQLSASLQA--L 62

Query: 342 GGDENEAAIFSAHLALLEDPGL-LDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLL 400
               +  A+  A L  L+DP L    AD +      A  +  R    Q   L+AL +  L
Sbjct: 63  DSQSDAYALVEADLLYLDDPDLRAHIADTITQLQFSACVSIERVFAHQASELEALDDPYL 122

Query: 401 AERANDLRDLEKRVLRVLLG----DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCM 456
           A+RA D+R L KR+++ + G    +   L+VP   I+ A +I+P++ A L     AG+ +
Sbjct: 123 AQRAEDVRSLGKRLIQAVFGHPGQEPGKLKVPT--ILLADDISPAEFAVLPLENVAGIVL 180

Query: 457 AEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVAL 516
             GG TSH AILAR+ G+P L++     L +  G Q+ +D   G L  +P+   LE   L
Sbjct: 181 KSGGLTSHTAILARAAGIPALLSCPYSELGINNGDQLAIDGDAGALYRNPEGGTLE--LL 238

Query: 517 QVAQREEQRRRQQADAQRE--ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEF 574
           +  +   +  R+Q D  R+  A+T+DG  I + ANV +  +  +    GADG+GLLRTEF
Sbjct: 239 RQHEASARLAREQLDQYRDKPAMTQDGHEISLLANVGNLNDVLKVSGLGADGIGLLRTEF 298

Query: 575 LFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRG 634
           + +     PDE  Q   Y + + A+  R + IRT+D+G DK L  L    EENPALGLRG
Sbjct: 299 MLMHSATLPDERAQYQLYSDAIHALEGRVLTIRTLDIGADKELPCLCQVKEENPALGLRG 358

Query: 635 IHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLP 694
           I    A P+LL  QLRA+LR       R++ PMV++V+EL A+   L     +L  E   
Sbjct: 359 IRYTLANPQLLKTQLRAVLRAANHGHVRLMFPMVNQVEELDAVLALLETCRRELDDEEKG 418

Query: 695 ----ELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPA 750
                LG+++E P+A L    +    DF+SIGTNDL+QYA+A DR +  LA    AL PA
Sbjct: 419 FGDISLGIVVETPAAVLNLPAMLPMLDFVSIGTNDLTQYAMAADRGNPCLARDYPALSPA 478

Query: 751 LLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQL 810
           +LRLI+ T   A      V +CG + SDP   P+L+GLG +ELSV    + E+K  + + 
Sbjct: 479 VLRLISMTLQSARSQDVKVSLCGEMGSDPRLVPLLIGLGFDELSVNVGAMLEVKAAICRQ 538

Query: 811 DAAECRRHAQALLDLGSARAVRDACLQHW 839
           +   C + A   L +    +  DAC+  +
Sbjct: 539 EFDRCTQLAGRAL-MADRLSELDACISSY 566


Lambda     K      H
   0.319    0.136    0.390 

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: 1093
Number of extensions: 44
Number of successful extensions: 3
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: 842
Length of database: 567
Length adjustment: 39
Effective length of query: 803
Effective length of database: 528
Effective search space:   423984
Effective search space used:   423984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources