Alignments for a candidate for nagF in Skermanella stibiiresistens SB22

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Skermanella stibiiresistens SB22

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_037459605.1 N825_RS29030 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_000576635.1:WP_037459605.1
          Length = 841

 Score =  452 bits (1163), Expect = e-131
 Identities = 280/673 (41%), Positives = 376/673 (55%), Gaps = 25/673 (3%)

Query: 175 QVRIAHRGGLHARPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVS 234
           +V +    GLHARPA++    A+ F S  ++   GK+A+  S++ M+ L +     + +S
Sbjct: 167 EVEVTGGTGLHARPASIFVTLAKQFNSDIRVSHQGKTANGKSMVSMLRLGVESGGVISIS 226

Query: 235 CRGSDAEAALQALLTTLSTALVEE---AHAS---APPPEP-----PRANAEE--GVLHGV 281
             G DAE AL  L+  + + L EE   AHA+   AP  +P     P A  ++  G++ GV
Sbjct: 227 ADGPDAEKALHTLIDAVESGLGEEDEAAHAAPKAAPDVQPAGQAIPHATPDDEPGLIRGV 286

Query: 282 CAAPGLVTGPLVRLSGIQLPEDIGGHAIEEQRQRLS-----DALAQVRGEIHLTLEHARA 336
            AAPG+   PL +L   Q+ EDI  HAI    +R       D       E+H T+E    
Sbjct: 287 AAAPGIAIAPLHQLRK-QVEEDIERHAINSDAERADFDHAIDRAGAELDELHRTVER--- 342

Query: 337 RQHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLA 396
           R    E  IF+AH   L+DP L+DA    I  G  A +AW  +I+ + + L  L   LLA
Sbjct: 343 RAGEMEARIFAAHREFLDDPDLIDAVRHRIGLGETAAYAWRETIEERAEDLAGLSDPLLA 402

Query: 397 ERANDLRDLRQRVLRVLLGEAWQFDVAAG--AIVAAQELTPSDLLQLSAQGVAGVCMVEG 454
            RANDLRD+  RVLR+L+    Q         I+ A++LTPSD   L    V G+    G
Sbjct: 403 GRANDLRDVGARVLRLLIRRNEQESNLPDHEIILVAEDLTPSDTASLDPDLVKGILTALG 462

Query: 455 GATSHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTPTVERLAQVRQAQT 514
           G  SH AILAR   +P +V  G E+L    G   VLD   G +   P   RL   R AQ 
Sbjct: 463 GPNSHTAILARSLDIPAVVGAGHEVLDLATGVTAVLDGSRGTVLPDPDAARLETARSAQH 522

Query: 515 RRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDR 574
                RA+    A+ PA T+DG  VEVAAN+ +  EAG ++  G + VGLLRTEFLF DR
Sbjct: 523 GAGQRRAEVLQAAYRPAITIDGHRVEVAANIGAVPEAGRAVQAGGEAVGLLRTEFLFQDR 582

Query: 575 HTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQ 634
              P EEEQ +AY+A+ EA+G  P+I+RT+D GGDK L Y+ +  E NP LG RGIRL+ 
Sbjct: 583 TDPPSEEEQYEAYRAMAEALGGLPLIVRTLDAGGDKPLPYIAMAHEDNPFLGQRGIRLSF 642

Query: 635 VRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDELLHIRKRLDALGSELGLSERPQLGVM 694
             PDL   QLRA+L+       +I+ PM+T V E    R  ++ +  E+   E   +G+M
Sbjct: 643 TMPDLFRSQLRAILRAASHGEIKIMFPMITSVAEFRRGRALVEEIRREVDGPE-IDVGIM 701

Query: 695 VEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC 754
           VEVP++A++A+ LA   DF SIGTNDL+QYTLAMDR H  LA   D LHPA+LR++ QT 
Sbjct: 702 VEVPSSAVMADLLAREVDFFSIGTNDLTQYTLAMDRGHPALAREADGLHPAVLRMVDQTV 761

Query: 755 AGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLS 814
             A   G+WVGVCG LA+DP+A P+LIGL V ELSV  P I  +K ++R +       L+
Sbjct: 762 RAAHGEGKWVGVCGNLAADPVAAPILIGLDVDELSVGVPNIPALKAQIRSMAYEDAKDLA 821

Query: 815 NELLNLGSALAVR 827
              L    A  VR
Sbjct: 822 RRALACDGAAEVR 834


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: 1565
Number of extensions: 79
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: 837
Length of database: 841
Length adjustment: 42
Effective length of query: 795
Effective length of database: 799
Effective search space:   635205
Effective search space used:   635205
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: 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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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