Alignments for a candidate for nagF in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_068174654.1 HTA01S_RS20310 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_001592305.1:WP_068174654.1
          Length = 588

 Score =  287 bits (735), Expect = 1e-81
 Identities = 196/544 (36%), Positives = 281/544 (51%), Gaps = 39/544 (7%)

Query: 312 EQLQALDRALEQVRSEIRETLSHAKK--------HKHTEEEQIFAAHLALLEDPALLEAA 363
           +Q  A    L Q R+ + E +   ++          H E   +   HL LL+D  L+   
Sbjct: 37  DQTTAEIERLRQARNAVMEEIVRVQQGLGELGSNDAHPELSALLDVHLMLLQDEQLISGV 96

Query: 364 IQSI-DQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRALLG------ 416
              I D+   A  A +  +E       ++ +P L ER  DL  + +R+LR + G      
Sbjct: 97  KHWIVDRHYNAEWALTTQLEVIARQFDEMEDPYLRERKADLEQVVERMLRFMRGVASPIM 156

Query: 417 ------------QDWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAIL 464
                        D   DVP   ++ AH+L+P+D+LQ  Q   AG     GG TSH AI+
Sbjct: 157 APVRTEARRDAAHDSVVDVPL--VLIAHDLSPADMLQFKQSVFAGFVTDVGGKTSHTAIV 214

Query: 465 ARGKGLPCLV-ALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRER 523
           AR   +P +V A SAS L + Q   V++D D G + + P    L +    QR+    RER
Sbjct: 215 ARSMDIPAVVGARSASHLVE-QDDWVIIDGDAGVVLVDPSPVLLAEYGFKQRQGEVERER 273

Query: 524 QQAQAHTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQ-TAPDEQ 582
                +TPA T DG RIE+ AN+   ++A  ALK GA GVGL RTEFLF+ R    PDE+
Sbjct: 274 LSRLKNTPAVTLDGQRIELQANIEQPDDAVAALKAGAVGVGLFRTEFLFMGRNGKLPDEE 333

Query: 583 EQRQAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPA---EANPVLGLRGIRMAQVRPE 639
           EQ QAY+  ++ M    V IRT+DVG DK LD  P+ A     NP LGLR IR +   P 
Sbjct: 334 EQYQAYRRAVEGMQGLPVTIRTVDVGADKPLDRTPVRAGEDHLNPALGLRAIRWSLADPA 393

Query: 640 LLDQQLRALLQVSPLQRCRILLPMVTEVDE----LLYIRQRLDALCAELALTQRLELGVM 695
           +   QLRA+L+ +      +L+PM+    E    L+ + +  + L     +   + LG M
Sbjct: 394 MFLAQLRAILRAAAHGSVNLLIPMLAHASEIRQTLVLVDRAREQLNTRGQVYGPVRLGAM 453

Query: 696 IEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC 755
           IE+PAAAL       H DFLSIGTNDL QYTLA+DR    +A   D +HPA+L+L+A T 
Sbjct: 454 IEIPAAALTIPLFLRHFDFLSIGTNDLIQYTLAIDRADEAVAHLYDPVHPAVLQLLASTI 513

Query: 756 IGAAKHQRWVGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFS 815
                  + V VCG +A D   T +L+GLG+   S+ P Q+  +K+++ + D A  + ++
Sbjct: 514 AQCRAQGKGVSVCGEMAGDVTMTRLLLGLGLRTFSMHPSQILAVKQQILRSDTARLQVWA 573

Query: 816 ATLL 819
            ++L
Sbjct: 574 QSVL 577


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: 1083
Number of extensions: 54
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 838
Length of database: 588
Length adjustment: 39
Effective length of query: 799
Effective length of database: 549
Effective search space:   438651
Effective search space used:   438651
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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:

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