Alignments for a candidate for nagF in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Acidovorax sp. GW101-3H11

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate Ac3H11_2115 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2115
          Length = 585

 Score =  270 bits (691), Expect = 1e-76
 Identities = 189/572 (33%), Positives = 282/572 (49%), Gaps = 33/572 (5%)

Query: 278 LHGVCAAPGLVTGPLVRLSGIQLPEDIGGHAIE-EQRQRLSDALAQVRGEIHLTLEHARA 336
           +HG+  A G+  G  V ++  ++  D+  + +E  Q +   + + Q R  +   L+  + 
Sbjct: 5   VHGLAVARGIAIGRAVLVASSRV--DVAHYFVEPSQVEGEIERVRQGRNAVVEELQRLQT 62

Query: 337 RQHRDEE----AIFSAHLALLEDPVLLDAADLFI-EQGSAAPHAWSRSIDTQCQVLQQLG 391
               D      A+   HL LL+D  L      +I E+   A  A +  ++   +   ++ 
Sbjct: 63  DMPTDAPHELTALLDVHLMLLQDEALTGGVKHWITERLYNAEWALTTQLEVIARQFDEME 122

Query: 392 STLLAERANDLRDLRQRVLRVLLGEAWQFDVAAGA-------------------IVAAQE 432
              L ER  DL  + +R+LR + G A      A +                   ++ A +
Sbjct: 123 DEYLRERKADLEQVVERILRHMKGVASPVAPPASSPRRKTQQDLLLDDTVDVPLVLVAHD 182

Query: 433 LTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDA 492
           L+P+D+LQ      AG     GG TSH AI+AR   +P +V          Q   V++D 
Sbjct: 183 LSPADMLQFKQSVFAGFVTDVGGKTSHTAIVARSMDIPAVVGARAASQLVRQDDWVIIDG 242

Query: 493 DGGRLELTPTVERLAQVRQAQTRRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAG 552
           D G + + P+   LA+    Q +    R +   L HTPA T+DG ++E+ AN+    +A 
Sbjct: 243 DAGVVIVDPSPIILAEYGFRQRQVELERERLARLRHTPAITIDGHKIELLANIEQPGDAA 302

Query: 553 ESLANGADGVGLLRTEFLFVDRH-TAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQ 611
            ++  GA GVGL R+EFLF+ +    P E+EQ +AY   ++ M   PV IRTIDVG DK 
Sbjct: 303 AAVRAGAVGVGLFRSEFLFMGKSGNLPGEDEQYRAYCEAIDGMQGLPVTIRTIDVGADKP 362

Query: 612 LDYLPLPSE-ANPVLGLRGIRLAQVRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDELL 670
           LD         NP LGLR IR +   P +   QLRA+L+     +  +L PM+    E+ 
Sbjct: 363 LDNKAHKDNYLNPALGLRAIRWSLADPAMFRTQLRAVLRAAAHGKVNLLFPMLAHTHEIQ 422

Query: 671 HIRKRLDALGSELGLSERP----QLGVMVEVPAAALLAEQLAEHADFLSIGTNDLSQYTL 726
               ++D   +EL     P    QLG M+EVPAAAL+     ++ DFLSIGTNDL QYTL
Sbjct: 423 QTLAQVDLARAELDARGEPYGPVQLGAMIEVPAAALMVRTFLKYFDFLSIGTNDLIQYTL 482

Query: 727 AMDRDHAGLAARVDALHPALLRLIAQTCAGAAKHGRWVGVCGALASDPLATPVLIGLGVR 786
           A+DR    +A   D LHPA+LRL+    A   + G+ V VCG  A D   T +L+GLG+R
Sbjct: 483 AIDRADEAVAHLYDPLHPAVLRLVGDVIAEGERQGKSVCVCGETAGDVTMTRLLLGLGLR 542

Query: 787 ELSVSPPQIGEIKDRVRHLDAAQCARLSNELL 818
             S+ P QI  IK  V   D  + A  + +++
Sbjct: 543 SFSMHPAQILAIKQEVLRADTRKLAPWAQQVI 574


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: 978
Number of extensions: 43
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: 837
Length of database: 585
Length adjustment: 39
Effective length of query: 798
Effective length of database: 546
Effective search space:   435708
Effective search space used:   435708
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: 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
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