Alignments for a candidate for manP in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for manP in Williamsia sterculiae CPCC 203464

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate WP_076477611.1 BW971_RS05975 PTS transporter subunit EIIA

Query= BRENDA::O31645
         (650 letters)



>NCBI__GCF_900156495.1:WP_076477611.1
          Length = 684

 Score =  335 bits (858), Expect = 5e-96
 Identities = 200/496 (40%), Positives = 286/496 (57%), Gaps = 49/496 (9%)

Query: 2   KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61
           +L+AIT+CP GIAHTYMAA+ L+ AA+R GV + VETQG            IR+ADA+I 
Sbjct: 176 RLVAITACPTGIAHTYMAADALKFAAERAGVDLVVETQGS-SANTPTDPSVIRDADAVIF 234

Query: 62  AADRSV-NKDRFIGKKLLSVGVQDGIRKPEELIQKALN--GDIPVYR-------SATKSE 111
           A D  V N+DRF GK +++ GV+  I +P+ +I +A+   GD    R       +AT S 
Sbjct: 235 ATDVGVKNRDRFAGKPVIASGVKRAINEPDVMIAEAVAAAGDPDASRVGGDTAAAATAST 294

Query: 112 SGNHQEKKQNPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEK---TPKGLVIPDDSFW 168
           +G         + + L+ GVS+M+PF+  GGLLIA+   LGG K    P G     ++  
Sbjct: 295 AGGDLGWGTR-LRQVLLTGVSYMIPFVAAGGLLIALGFLLGGYKIALAPPGSADGTEAIG 353

Query: 169 KTIE----------------------QIGSASFSFMIPILAGYIAYSIADKPGLVPGMIG 206
           KTI                        +G  +FSF++P LAGYIAY+IAD+PGL PG   
Sbjct: 354 KTIALSNSLWNLPSGGLAQYLGAICFTLGGLAFSFLVPALAGYIAYAIADRPGLAPGFTA 413

Query: 207 GYIAATGSFYDSASGAGFLGGIIAGFLAGYAALWIKKLKVPKAIQPIMPIIIIPVFASLI 266
           G +A          GAGF+GG++ G L G+ ALW+ ++ +P   + +MP++IIP+ A+L 
Sbjct: 414 GAVAVF-------VGAGFIGGLVGGLLGGFVALWVGRIPLPAWARGLMPVVIIPLLATLA 466

Query: 267 VGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSILLALILGAMISFDMGGPVNKVAFLFGS 326
            G      +G P+A +  SLT WL G+ G+S+I+L +ILG M+ FD+GGPVNK A+ F  
Sbjct: 467 TGGIMFLFLGRPLAWVNTSLTDWLNGLSGTSAIILGIILGLMMCFDLGGPVNKAAYAFAV 526

Query: 327 AMIGEGN---YEIMGPIAVAICIPPIGLGIATFLGKRKFEASQREMGKAAFTMGLFGITE 383
             +  G+     IM  +  A  +PP+ L +AT L  R F   +RE GKAA+ +G   I+E
Sbjct: 527 QGLSSGDPAQLRIMAAVMAAGMVPPLALALATALRPRLFTEPERENGKAAWLLGASFISE 586

Query: 384 GAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDRVAHGGPIVAVLGAVDHVLMFFIAV 443
           GAIPFAA DPLRVIPS+MAG      + M  +V  R  HGG  + V  A+ +V  F +++
Sbjct: 587 GAIPFAAVDPLRVIPSMMAGGAVTGALVMAFDVTLRAPHGG--IFVFFAMGNVFGFLLSL 644

Query: 444 IAGSLVTALFVNVLKK 459
           + G +++A  V  LK+
Sbjct: 645 LVGMVISATLVLALKQ 660



 Score = 77.0 bits (188), Expect = 3e-18
 Identities = 45/146 (30%), Positives = 84/146 (57%), Gaps = 3/146 (2%)

Query: 504 DIISPELIEPNL-SGETSDDIIDELIQKLSRRGALLSESGFKQAILNREQQGTTAIGMNI 562
           +II+ +L+  ++ +G    ++ID L+++L+  G +       +A + RE Q  T +   I
Sbjct: 4   NIITTDLVALDVDAGAEKSEVIDFLVERLAADGRVHDTVAVNEAAMAREAQSATGLPGGI 63

Query: 563 AIPHGKSEAVREPSVAFGIKRSGVDWNSLDGSEAKLIFMIAVPKESGGNQHLKILQMLSR 622
           AIPH ++E V    ++F      VD+ + DG  A L+F+IA P  SGG+QH+K+L  L+R
Sbjct: 64  AIPHCRTEGVSAAGLSFARLAPAVDFGAKDG-PADLVFLIAAP-ASGGSQHMKLLSSLAR 121

Query: 623 KLMDDNYRERLLSVQTTEEAYKLLEE 648
            L+  ++   L + ++ +E   L+++
Sbjct: 122 ALVRPDFVTSLRNAKSADEVVALVDQ 147


Lambda     K      H
   0.319    0.137    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: 995
Number of extensions: 62
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 650
Length of database: 684
Length adjustment: 38
Effective length of query: 612
Effective length of database: 646
Effective search space:   395352
Effective search space used:   395352
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 (21.7 bits)
S2: 54 (25.4 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