Alignments for a candidate for nagF in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Shewanella amazonensis SB2B

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate 6936677 Sama_0864 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_17540
         (837 letters)



>FitnessBrowser__SB2B:6936677
          Length = 744

 Score =  278 bits (710), Expect = 1e-78
 Identities = 191/556 (34%), Positives = 292/556 (52%), Gaps = 14/556 (2%)

Query: 280 GVCAAPGLVTGPLVRLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQH 339
           GV  A  LV G  + L   + PE      ++ +  RL  A+ + R  +   L       H
Sbjct: 178 GVAIAHALVIGGEISL---EQPEACATD-VDAEVNRLRLAMGRSRDAL-TALAQKFENDH 232

Query: 340 RDE-EAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAER 398
            DE  +IF++  +LLED  L       +  G +A  A SR         + +    L ER
Sbjct: 233 DDELSSIFTSLQSLLEDASLGGEYQREVLAGWSAETAVSRVSLRYVAQFETMEDAYLRER 292

Query: 399 ANDLRDLRQRVLRVLLGEA-WQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGAT 457
           A+D+RDL QRVLR L+       D     I+  +E   S L +   Q +AG+    GG  
Sbjct: 293 ASDIRDLGQRVLRQLIEPGRMMLDPDKPVILVTREADTSMLAEFPRQKLAGIVTEAGGVN 352

Query: 458 SHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQTRRT 517
           SH AILAR  G+P ++ +   L A    Q +VL+A  G L ++P+   + + R   + + 
Sbjct: 353 SHAAILARALGVPAIMGVEQVLQANLDKQLLVLNASRGILMVSPSPTVVDEYRNLISAQK 412

Query: 518 ALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDRHTA 577
           AL  Q       PA T+DG  + +  N    +     +A+GADGVGL RTE  F+ +   
Sbjct: 413 ALDRQYAEELKEPALTLDGHRIHLYLNAGLMSGVSSEIADGADGVGLYRTEIPFMLQQRF 472

Query: 578 PDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQVRP 637
           P E EQ + Y++VL++   +PV++RT+DVGGDK L Y P+ SE NP LG RGIRL+   P
Sbjct: 473 PSESEQIKVYRSVLQSAAGRPVVMRTLDVGGDKPLPYFPI-SEENPFLGWRGIRLSLDHP 531

Query: 638 DLLDQQLRALLQTR-PLDRCRILLPMVTEVDELLHIRKRLDALGSELGLS-----ERPQL 691
           +L   QLRA+LQ     D  +ILLPMV+ +DE+      LD   SEL         RP +
Sbjct: 532 ELFLVQLRAMLQAAGDTDNLKILLPMVSSLDEIDEALLYLDQAFSELRADVNPSLARPPV 591

Query: 692 GVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIA 751
           GVM+EVPA      ++A+  +F+S+G+NDL+QY LA+DR++  +++  D+ HP +LR + 
Sbjct: 592 GVMLEVPALLYQLREVAQRVEFVSVGSNDLTQYLLAVDRNNPRVSSLYDSYHPGVLRALQ 651

Query: 752 QTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCA 811
                  +H   V VCG LA +P+   +L+ +G  ELS++   + +I   +R ++ ++  
Sbjct: 652 LALQECRQHKLDVSVCGELAGEPMGALLLVAMGYDELSMNQGSLAKINYLLRRVERSELE 711

Query: 812 RLSNELLNLGSALAVR 827
           +L   ++ + +   VR
Sbjct: 712 QLLALVMQMSNGQDVR 727


Lambda     K      H
   0.319    0.134    0.386 

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: 1031
Number of extensions: 41
Number of successful extensions: 6
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: 837
Length of database: 744
Length adjustment: 41
Effective length of query: 796
Effective length of database: 703
Effective search space:   559588
Effective search space used:   559588
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 (21.8 bits)
S2: 55 (25.8 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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