Alignments for a candidate for nagF in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Moritella dasanensis ArB 0140

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_017220595.1 A923_RS0105175 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_04460
         (838 letters)



>NCBI__GCF_000276805.1:WP_017220595.1
          Length = 815

 Score =  352 bits (903), Expect = e-101
 Identities = 217/643 (33%), Positives = 342/643 (53%), Gaps = 13/643 (2%)

Query: 177 RIIHRGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCK 236
           R+ +  G+HARP+ALI  T    ++  +L    + A+  SL  +  L +   DE+ +   
Sbjct: 159 RVQNPHGIHARPSALIVATMAAIDATIELGRRDERANAKSLNSIAKLNVQCGDEICLYAS 218

Query: 237 GADAKAALQALLNAL------STAVNDDSHAAAPTPIAQRTRTAEAGVLNGVCAAPGLVG 290
           GA+A+ A+   +         S A +  S  A     +  ++    G L G+    G+V 
Sbjct: 219 GAEAELAIAEFIRLADGHFGESIANDIASVNAISNEYSVSSQEKVEGALTGLAVCGGIVT 278

Query: 291 GPLFQLAAI-PLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAA 349
           GP+    A+ P   +    + E +   LD A+++V  ++ +  S  +     E  +IF A
Sbjct: 279 GPVIHFDAVMPAIPERSFESVEMENIRLDSAIQKVTEQLVQQASDTELTLGKEHAEIFKA 338

Query: 350 HLALLEDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQR 409
           H+ +L DP LL      ++Q   A  AW ++     E  + L +  + ER  D++D+ ++
Sbjct: 339 HMIMLADPELLADVRLRVEQDMIAEQAWLEATALIAEQYRALKSTYMQEREADVKDIARQ 398

Query: 410 VLRALLG--QDWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARG 467
           V+  L G  Q    ++   +++ A +L PSD  QL  Q V  +C++ GG TSH  ILAR 
Sbjct: 399 VMLQLCGKSQGGRIELAQPSVLLAKDLLPSDTAQLDPQKVLAICLSGGGKTSHSVILARA 458

Query: 468 KGLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQ 527
            G+P ++ L   L     GQ V +D   G L LTP + + +++ + ++  L     Q   
Sbjct: 459 MGIPAIIRLENCLELVEPGQVVTVDGFSGLLWLTPTADKQQELEERRKTWLDHTSNQLLA 518

Query: 528 AHTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQA 587
           A  PA T DG R  V AN+    + + AL  GA+GVGLLRTEF+F      P EQ+Q   
Sbjct: 519 AQEPAMTTDGYRFNVMANIGGLEDVSAALDAGAEGVGLLRTEFMFQSHAELPSEQDQYIV 578

Query: 588 YQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRA 647
           Y+ +  A+G++ + IR++DVGGDK L   P+ AE NP LGLRG+R+      L   QLRA
Sbjct: 579 YRDIAAALGNRPLTIRSLDVGGDKPLLSYPMTAEDNPFLGLRGVRLCLADHILFKDQLRA 638

Query: 648 LLQV-SPLQRCRILLPMVTEVDELLYIRQRLDALCAELALTQR---LELGVMIEVPAAAL 703
           +L+V +     ++++PM+ +  EL+ ++  +     EL L +R   L +G+MIEVPAA  
Sbjct: 639 VLRVAAEHSNVQLMIPMIAQPSELIAVKTLVSTCREELGLPERDYPLAIGIMIEVPAAVF 698

Query: 704 LAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQR 763
            A++LA+ ADF SIGTNDL+QY +A DR +  +A  VD    A++  IA TC    K   
Sbjct: 699 NADELAQEADFFSIGTNDLTQYVMAADRGNPAVADLVDYKQQAVINAIAMTCEAGQKANI 758

Query: 764 WVGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQL 806
            VG+CG +A D   T +LI LG+++LS S   +  +K +VR++
Sbjct: 759 PVGMCGEMAGDSDMTELLIRLGVTKLSASASMIPGVKAKVRRI 801


Lambda     K      H
   0.318    0.133    0.379 

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: 1328
Number of extensions: 61
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: 838
Length of database: 815
Length adjustment: 42
Effective length of query: 796
Effective length of database: 773
Effective search space:   615308
Effective search space used:   615308
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

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 (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 2024 update 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