GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Hydrogenovibrio kuenenii DSM 12350

Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_024851899.1 N745_RS0109535 phosphomannomutase/phosphoglucomutase

Query= BRENDA::P26276
         (463 letters)



>NCBI__GCF_000526715.1:WP_024851899.1
          Length = 474

 Score =  434 bits (1116), Expect = e-126
 Identities = 226/467 (48%), Positives = 305/467 (65%), Gaps = 16/467 (3%)

Query: 13  IFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGL 72
           IF+AYDIRG V  +L    A  IG A   + +A GE C+ VGRDGRLS   L +  ++G+
Sbjct: 8   IFKAYDIRGKVDISLDESAAESIGIAFAEQLIAYGETCLVVGRDGRLSSLRLQQAFMRGV 67

Query: 73  VDCGCQVSDVGMVPTPVLYYAANVLEG-KSGVMLTGSHNPPDYNGFKIVVAGETLANEQI 131
                 + DVG V +P++Y+AA  LEG  S  ++TGSHNPP+ NG K+V  G+ L  +QI
Sbjct: 68  ASQKVSIIDVGEVTSPMVYFAAETLEGVNSCAVITGSHNPPEDNGIKLVTQGQALYGQQI 127

Query: 132 QALRERIE-----------KNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCG 180
           QALR+RI            KN    G  S + + I   Y ++I  +I + +P+KVVVD G
Sbjct: 128 QALRKRIGSEGFDQTLKQVKNLPGWGNSSAQNLSIFSDYRQRIASEIQLYRPLKVVVDAG 187

Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240
           NGVAG  AP+++ ++GC VI L+CEVDG+FPNHHPDP K ENL DL   V    ADLGLA
Sbjct: 188 NGVAGRYAPEVLRSIGCEVIELFCEVDGHFPNHHPDPAKLENLTDLKTAVFEHQADLGLA 247

Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300
           FDGDGDR GV+ N G ++ PDR L+LFA+D++    G +IIFDVKC+  +   +    G+
Sbjct: 248 FDGDGDRCGVIDNQGLVLEPDRQLILFARDILKNRAGGEIIFDVKCSALVAQEVEKSNGK 307

Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360
            VMWKTGHSL+K KMK T ALL GEMSGH+FF++RW+GFDD IY+AARL+E+L++  + +
Sbjct: 308 AVMWKTGHSLMKAKMKVTSALLGGEMSGHLFFQDRWYGFDDAIYTAARLVELLARQSQTA 367

Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEAL----QRDAQWGEGNITTLDGVRVDYPKG 416
             +F+  P   STPE++I V E     ++E L     +++      I TLDGVRV+Y  G
Sbjct: 368 AELFAKIPQWQSTPELHIDVPEGEANLLVENLCQSFMKESDSEIKEIITLDGVRVEYKDG 427

Query: 417 WGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463
           WGLVRASNTT  L +RFEA T++ LE+I+  F+ +L  +   L +PF
Sbjct: 428 WGLVRASNTTSTLTIRFEATTQQGLEKIQKRFKQRLLVLAPELKLPF 474


Lambda     K      H
   0.319    0.138    0.410 

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: 544
Number of extensions: 14
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: 463
Length of database: 474
Length adjustment: 33
Effective length of query: 430
Effective length of database: 441
Effective search space:   189630
Effective search space used:   189630
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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