GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_068170530.1 HTA01S_RS10525 glutamine synthetase family protein

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>NCBI__GCF_001592305.1:WP_068170530.1
          Length = 456

 Score =  560 bits (1443), Expect = e-164
 Identities = 267/446 (59%), Positives = 331/446 (74%), Gaps = 3/446 (0%)

Query: 2   HDIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPED 61
           +D++++L ++RVTE+E ++PD+ G+ARGKI+PR KF     MRLPQA++   VTG++PE 
Sbjct: 11  NDLENWLNEHRVTEVECLVPDLTGVARGKILPREKFTEDRGMRLPQAIVGMGVTGEFPES 70

Query: 62  GTLTGVTDP---DMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVL 118
           G    V DP   DM   PD +T+R++PWA DPTAQVIHDC    G  V  +PR VLRR+ 
Sbjct: 71  GPYYDVVDPTDKDMQLRPDPTTVRIVPWATDPTAQVIHDCFDHHGKLVPFAPRSVLRRIC 130

Query: 119 ELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLF 178
           +LY A+GW+PV+APELEFYL   N DP+  L+PPIGR+GR ET RQAYSI+AVNEFDPLF
Sbjct: 131 DLYAAEGWEPVVAPELEFYLTARNTDPNTLLKPPIGRSGRAETSRQAYSIDAVNEFDPLF 190

Query: 179 EDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYA 238
           E+IY+YC+  EL VDTLIHEVGA QMEINF H  PL LAD VF FKRTVREAALRH MYA
Sbjct: 191 EEIYDYCDKMELNVDTLIHEVGAGQMEINFFHAHPLGLADEVFFFKRTVREAALRHDMYA 250

Query: 239 TFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIF 298
           TFMAKP+ GEPGSAMH+HQS++D+ TG N+F+  DG  +  F  YI GLQ+Y PA M + 
Sbjct: 251 TFMAKPIAGEPGSAMHVHQSILDKATGKNIFSNEDGTASESFYHYIGGLQRYIPAAMVLV 310

Query: 299 APYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAA 358
           APY+NSYRRLSR  AAPIN+ WG+DNRTVG R P S PAARR+ENR+ G D NPY+A+A 
Sbjct: 311 APYVNSYRRLSRHTAAPINIEWGHDNRTVGIRSPISSPAARRVENRVIGADANPYVAMAM 370

Query: 359 TLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYL 418
           TLA GYLGM  K++    +  D Y  PY LPR+L E L  +     + EVLG++F+  Y 
Sbjct: 371 TLACGYLGMKNKIKPKPEMKGDAYLAPYSLPRSLGEALDWLRREPDLHEVLGKEFITIYT 430

Query: 419 ALKETEYEAFFRVISSWERRHLLLHV 444
            +KE E++ F +VIS WER HLLLHV
Sbjct: 431 EIKELEFDEFMKVISPWEREHLLLHV 456


Lambda     K      H
   0.321    0.138    0.418 

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: 723
Number of extensions: 31
Number of successful extensions: 3
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: 444
Length of database: 456
Length adjustment: 33
Effective length of query: 411
Effective length of database: 423
Effective search space:   173853
Effective search space used:   173853
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: 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