Alignments for a candidate for ans in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

Alignments for a candidate for ans in Erythrobacter marinus HWDM-33

Align glutaminase subunit (EC 3.5.1.38) (characterized)
to candidate WP_047092224.1 AAV99_RS01710 glutaminase A

Query= metacyc::MONOMER-13074
         (602 letters)



>NCBI__GCF_001013305.1:WP_047092224.1
          Length = 530

 Score =  421 bits (1081), Expect = e-122
 Identities = 217/481 (45%), Positives = 301/481 (62%), Gaps = 6/481 (1%)

Query: 95  ALKATGLQTSDPRLQDCMSKMQRMVQESSSGGLLDRELFQKCVSS-NIVLLTQAFRKKFV 153
           AL+  GLQ  DPRL     K+ +M       G LD +  +  +      L+ +A     +
Sbjct: 39  ALEEMGLQRDDPRLSSLFEKLDKM----PGSGTLDEDGLRSLLGEVEASLVGRALSGSLI 94

Query: 154 IPDFEEFTGHVDRIFEDAKELTGGKVAAYIPHLAKSNPDLWGVSLCTVDGQRHSVGHTKI 213
           IP FEEF   ++ IFE  +  + G VA+YIP LA+ +P+ + +++CT+DGQRHS+G  + 
Sbjct: 95  IPAFEEFRDQLNSIFETCRGESSGSVASYIPQLARVDPEKFAMAVCTIDGQRHSIGDDQD 154

Query: 214 PFCLQSCVKPLTYAISVSTLGTDYVHKFVGKEPSGLRYNKLSLNEEGIPHNPMVNAGAIV 273
            FC+QS  KP+ YAI+      D +H  VG+EPSG  +N+L+LN  G+PHNPM+NAGAI+
Sbjct: 155 RFCVQSTCKPVNYAIAHGLSNADSIHNHVGREPSGRSFNELTLNPAGLPHNPMINAGAIM 214

Query: 274 VSSLIKMDCNKAEKFDFVLQYLNKMAGNEFMGFSNATFQSEKETGDRNYAIGYYLKEKKC 333
            SSLIK   + A++FDFV+     + G    GF N  F SEK T DRN+A+ Y+++E   
Sbjct: 215 ASSLIKPRESLADRFDFVMSTWRDLGGGVEPGFDNTVFLSEKATADRNFALAYFMRENGA 274

Query: 334 FPKGVDMMAALDLYFQLCSVEVTCESGSVMAATLANGGICPITGESVLSAEAVRNTLSLM 393
           FP   D+M  LD YFQ CS+ +     + +AATLANGG+CP T + VL AEAVRN LSLM
Sbjct: 275 FPPNTDLMETLDFYFQCCSISIDVRHMATIAATLANGGVCPTTNQRVLDAEAVRNCLSLM 334

Query: 394 HSCGMYDFSGQFAFHVGLPAKSAVSGAILLVVPNVMGMMCLSPPLDKLGNSHRGISFCQK 453
           +SCGMYD+SG+FAF VG+PAKS VSGA++LV+P V G+   SP LD+ GNS RG+ F Q+
Sbjct: 335 YSCGMYDYSGEFAFTVGIPAKSGVSGALMLVIPGVCGIAIWSPRLDRCGNSVRGVRFAQE 394

Query: 454 LVSLFNFHNYDNLRHCARKLDPRREGGEVRNKTVVNLLFAAYSGDVSALRRFALSAVDME 513
           L   ++FH+Y  +      +DP +   E   +   +L  AA  GD+  LRR   S  D+ 
Sbjct: 395 LSKRYSFHSYATMVPGQELIDPTKSQAERVAEVASSLCSAASVGDLGELRRLVASGADIL 454

Query: 514 QKDYDSRTALHVAAAEGHIDVVKFLIEACKVNPFVKDRWGNIPLDDAVQFNHLEVVKLLQ 573
           Q DYD RTALH+AA+EG + VV+FL+ +   +   KDRWGN  L DA +    + V+LL 
Sbjct: 455 QADYDGRTALHLAASEGRVGVVRFLL-SIGADAEQKDRWGNTALADAEREGMGDAVQLLS 513

Query: 574 D 574
           +
Sbjct: 514 N 514


Lambda     K      H
   0.320    0.135    0.403 

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: 757
Number of extensions: 28
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: 602
Length of database: 530
Length adjustment: 36
Effective length of query: 566
Effective length of database: 494
Effective search space:   279604
Effective search space used:   279604
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 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