Alignments for a candidate for nagF in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Maridesulfovibrio zosterae DSM 11974

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_027722339.1 H589_RS0112545 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_000425265.1:WP_027722339.1
          Length = 829

 Score =  391 bits (1005), Expect = e-113
 Identities = 260/792 (32%), Positives = 407/792 (51%), Gaps = 50/792 (6%)

Query: 64  AVTLRADNGAELLLHLGL-------------DTVELQGEGFSMLVKEGTRVSNGQALLRF 110
           +V ++A++G  +++ LG              D V+ +    S  + EGT  +  QA +  
Sbjct: 57  SVAMQAEDGVLVMMDLGSALMSAETALDFLPDEVKAKVMLCSAPIVEGTMAAAVQASVGA 116

Query: 111 DLDQVAQGCKSLVSLLVLTNSEDFQVLPITLKSVKVGEPLLHIVPRTTHSAQVEADSSGA 170
            L +      + +++ +       Q+ PIT +S+   + +   +P            +G 
Sbjct: 117 SLQEAIAEASTAINVKIQ------QLAPITGESISTTDCVQEDMP------------TGE 158

Query: 171 EVHGHIRIIHRGGLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDE 230
           E+   + +I++ GLHARPAA +  TA  F S   +     SAS  S+  +  L +   D 
Sbjct: 159 ELSADLLVINKMGLHARPAANLVSTAGKFKSSVAIRKGADSASAKSINQVALLSVKNGDT 218

Query: 231 VQVSCKGADAKAALQALLNALSTAVNDDSHAAAPTPIAQRTRTAEAGVLNG---VCAAPG 287
           + +S  GADA+ A  AL+      ++ D+       +A+     +  V  G   +  APG
Sbjct: 219 ITISVSGADAQEAFDALIK-----LHKDNFGERDEDVAELVEDIKPVVQAGDGTIVGAPG 273

Query: 288 ----LVGGPLFQLAAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEE 343
                VG      A +P  E     + E +L+ LD A+    S+I+      +K      
Sbjct: 274 SGGYAVGTAYVHQATLPEVERKNISDVETELEKLDLAISTALSDIKILQRETEKTSGKAN 333

Query: 344 EQIFAAHLALLEDPALLEAAIQSI-DQGSAATHAWSQSIEAQCEVLQQLGNPLLAERAND 402
             IF  H  ++ D  + + A + + +Q   A +AW + +       + L +  +  RA D
Sbjct: 334 AAIFEVHAMIISDKDMRDKAAEIVSEQQINADYAWFEVMNKITADYRNLDDTYMQARAAD 393

Query: 403 LRDLRQRVLRALLGQDWH-YDVPAGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHV 461
           + D   RVLR L G++     +  GAI+ AH+L+PSD+  L  + V G+    GG TSH 
Sbjct: 394 VMDCGGRVLRILAGEEEQGICLENGAIIVAHDLSPSDVAGLDLEKVLGVVTEIGGVTSHA 453

Query: 462 AILARGKGLPCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRR 521
           AIL+R  G+P ++    S+ Q   G  + L+   G +   P+   +  +A+ +   L  R
Sbjct: 454 AILSRSMGIPAVIGAGKSIQQIQNGTIIALNGFEGVIWPEPEQSVVNDIAEKRVLWLAER 513

Query: 522 ERQQAQAHTPAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDE 581
           E  +A+   PA T DG  I V  N+    +A    + GA+GVGL RTEFLF DR  AP E
Sbjct: 514 EEAKAKGAAPAKTLDGTDIMVMGNIGVPADAPRVFEYGAEGVGLFRTEFLFQDRSQAPTE 573

Query: 582 QEQRQAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELL 641
            EQ  AY     AM    VIIRT+D+GGDK + YL  P E NP LG RGIR    RPEL 
Sbjct: 574 DEQFDAYVEAARAMQGNPVIIRTLDIGGDKPVKYLDTPEEDNPFLGERGIRFCMARPELF 633

Query: 642 DQQLRALLQVSPLQRCRILLPMVTEVDELLYI----RQRLDALCAE-LALTQRLELGVMI 696
             QLRALL+ +  +   I+ PM+++VDEL  +     Q  + L +E + + ++++ G+MI
Sbjct: 634 RTQLRALLRAASEENIWIMYPMISDVDELSSVLEIQNQAREVLVSEGVKIAEKIKTGIMI 693

Query: 697 EVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCI 756
           EVPAA  +A++LA+  DF SIGTNDL+QY +A DR +A ++   D L+PA+LR++A TC 
Sbjct: 694 EVPAAVAVADKLAQKCDFFSIGTNDLTQYVMAADRGNASVSKLCDNLNPAVLRMVAMTCD 753

Query: 757 GAAKHQRWVGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSA 816
            A K    VG+CG LA +  A+ +L+GLG+ ELS++ P + E+KE +R ++  DCR  + 
Sbjct: 754 AAKKAGIEVGMCGELAGNSKASALLLGLGLDELSMNGPAIPEVKEAIRSVNMDDCRALAQ 813

Query: 817 TLLNLSSATAVR 828
            +L  +S+  VR
Sbjct: 814 KVLEANSSDEVR 825


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: 1280
Number of extensions: 41
Number of successful extensions: 4
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: 829
Length adjustment: 42
Effective length of query: 796
Effective length of database: 787
Effective search space:   626452
Effective search space used:   626452
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 Apr 09 2024. 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 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