Alignments for a candidate for nagF in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Chromobacterium vaccinii MWU205

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_046156291.1 VL52_RS06575 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>NCBI__GCF_000971335.1:WP_046156291.1
          Length = 831

 Score =  782 bits (2020), Expect = 0.0
 Identities = 434/844 (51%), Positives = 552/844 (65%), Gaps = 22/844 (2%)

Query: 10  LLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCDATVTHLARTGHAVTLAT 69
           LLAP +GP + L  VPDPVF+G M GDG+ +DPL   L+APC   V  LARTGHA+T+A 
Sbjct: 7   LLAPFSGPAIALDRVPDPVFAGRMMGDGLAIDPLSPTLLAPCSGAVAQLARTGHALTIAA 66

Query: 70  AEGAEILLHIGIDTVELNGKGFAPMVAQGAHVRAGDVLIEFDQDQVALNAPSLVSVIAIA 129
             GAE+L+HIGIDTV+L G+GF P+VA G  V+AG  LIE D D VA  APSL +++ IA
Sbjct: 67  DNGAEVLIHIGIDTVKLEGRGFRPLVAVGDRVQAGQPLIEVDLDAVARQAPSLQTMVVIA 126

Query: 130 NSDAFEIVERVQGGLLKAGETPLLVLRARDGAAAEASRQLSSTNVTEEARQQVTLVHAGG 189
           NSD F    R +G LL+AG +  L+L AR+  +   S          E R + T+ H GG
Sbjct: 127 NSDQFSFPRRAEG-LLEAGRSHFLILAAREAVSPCESAG------GPERRGEATVRHEGG 179

Query: 190 LHARPAARAREAARGFDARVEVRYEGRKAAIESVVGLLGLGAGEGATVELLGMGPQAAAA 249
           LHARP+A  ++AA+   A V +   G++A   SVV L+GLG  EG  V ++  G  A AA
Sbjct: 180 LHARPSALVQQAAKRHAAEVSIELSGKRANARSVVALMGLGVAEGDRVAVIVSGHDADAA 239

Query: 250 VAAIANEL-TREAHGEVEEKPARQSSPAPQAVARPAGETLAPNTLAGVCAAPGVAVGKLV 308
           +AA+   L TR   G     PA+   P                 LAGV AAPG+A+G++V
Sbjct: 240 LAAVIEALQTRSEAGHAAAAPAQAREPVA-------------GYLAGVAAAPGLAIGRVV 286

Query: 309 RWDDADIDPPEKANGTSAAESRLLDKAIATVDADLDTTVRDASQRGAVGEAGIFSVHRVL 368
           R D  ++  PE+  G  A E   L  A+A V   + + +  A +RGA  E+ IF+ H  L
Sbjct: 287 RLDAFEMPLPEQGGGI-AEERAALTSALARVRGAISSGIDVALRRGATAESDIFAAHLAL 345

Query: 369 LEDPTLLDAARDLISLGKSAGFAWREAIRAQIAILTNIEDALLAERAADLRDIEKRVLRA 428
           L+DP LL AA   I  G+ AGF +R A+RAQ AIL  + + LLAER ADL+DIE++VL A
Sbjct: 346 LDDPELLSAAEADIDAGRGAGFGFRRAVRAQCAILAGLGNQLLAERVADLKDIERQVLVA 405

Query: 429 LGYTSATARTLPEEAVLAAEEFTPSDLSTLDRSRVTALVMARGGATSHAAILARQAGIPA 488
           L         L + ++LAAE+  PS+L+ L R +V  +V A GGA+ H AILAR  GIPA
Sbjct: 406 LYGEPEQGPELFDASILAAEDLAPSELTRLPRGKVAGIVTAAGGASGHVAILARALGIPA 465

Query: 489 LVAVGDALHAIPEGTQVVVNATTGRLEFAPTELDVERARLERTRLADVREANRRTSQQAA 548
           LVA G +  A+ +G  +V++A  G     P+  D+  AR E  +L   R A + ++   A
Sbjct: 466 LVACGPSALALEQGQTLVLDARAGLANPQPSAADLAAARAEIDKLEAKRRAMQASANAPA 525

Query: 549 VTSDGRAIEVAANIATLDDAKTAVENGADSVGLLRTELLFIHRAAAPTTDEHRQSYQAIV 608
           +T DG AIEVA NIA  DDA+  V +GAD+VGLLRTE LFI R  APT  E  ++YQA++
Sbjct: 526 ITVDGVAIEVAVNIANADDAREGVAHGADAVGLLRTEFLFIDRRDAPTEAEQTEAYQAVL 585

Query: 609 DALSGRTAIIRTLDVGADKEVDYLTLPPEPNPALGLRGIRLAQVRPDLLDDQLRGLLAVQ 668
           DAL GR AIIRTLDVG DKEV YL LPPEPNPALGLRGIR     PD+LD QLR LLAV+
Sbjct: 586 DALDGRNAIIRTLDVGGDKEVPYLQLPPEPNPALGLRGIRTGFAYPDMLDTQLRALLAVK 645

Query: 669 PLGAVRILLPMVTDVGELIRIRKRIDEFARELGRTEPIEVGVMIEVPSAALLADQLAQHA 728
           PL  +RIL+PM+ DVGELIR+R+RI++ A  +   E  ++GVM+EVPSAALLADQLA+HA
Sbjct: 646 PLSRLRILVPMIADVGELIRLRERIEQLAGAMNLAERPQLGVMVEVPSAALLADQLARHA 705

Query: 729 DFLSIGTNDLTQYTLAMDRCQADLAAQADGLHPAVLRLIAATVQGADKHGKWVGVCGALA 788
           DFLSIG+NDLTQYTLAMDRC A LA++ D +HP +LRLIA TV+GA KHGKWVGVCGA+A
Sbjct: 706 DFLSIGSNDLTQYTLAMDRCNATLASRIDSMHPGLLRLIAITVEGAKKHGKWVGVCGAMA 765

Query: 789 GDPLAMPLLVGLGVTELSVDPVSVPGIKARVRNLDYQLCRQRAQDALALESAQAVRAASR 848
            DP A+P+L+GLGV ELSV P  VP +K+ VR L  + C + A   LAL S QAVR    
Sbjct: 766 SDPQAVPVLIGLGVAELSVSPRLVPEVKSLVRGLSRRHCEEEALRLLALGSPQAVRGRVT 825

Query: 849 ETWP 852
           E WP
Sbjct: 826 ELWP 829


Lambda     K      H
   0.317    0.133    0.371 

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: 1692
Number of extensions: 83
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: 854
Length of database: 831
Length adjustment: 42
Effective length of query: 812
Effective length of database: 789
Effective search space:   640668
Effective search space used:   640668
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.

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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