Aligments for a candidate for hglS in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for hglS in Pseudomonas simiae WCS417

Align putative hydrolase, required for lysine catabolism (characterized)
to candidate GFF3040 PS417_15555 hypothetical protein

Query= reanno::pseudo5_N2C3_1:AO356_01105
         (458 letters)



>FitnessBrowser__WCS417:GFF3040
          Length = 458

 Score =  698 bits (1801), Expect = 0.0
 Identities = 355/453 (78%), Positives = 385/453 (84%), Gaps = 3/453 (0%)

Query: 4   VSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVLSEQPQLAEHLRSTGELERLD 63
           VSPD IR+ FS+AMSDMYRDEVPLYGALM+LV  TNA VL  QPQLA+ L+ TGE++RLD
Sbjct: 7   VSPDQIRRGFSKAMSDMYRDEVPLYGALMELVAETNAHVLDTQPQLAQQLQRTGEIQRLD 66

Query: 64  LERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQVSPF 123
           +ERHGAIR+GTAAELAT+ RLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHE ALQ SPF
Sbjct: 67  MERHGAIRLGTAAELATISRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHEQALQTSPF 126

Query: 124 RVFTSLLRLELIENSELRAFAESVLAKRQIFTPGALALIDLAERQGGLTQAQAEDFVLQA 183
           RVFTSLLRLELIEN +LRAFAE+ LAKR IFT GAL LI+ AE+ GGL    A++F+ QA
Sbjct: 127 RVFTSLLRLELIENPDLRAFAETALAKRSIFTRGALTLIEQAEKDGGLNAEDADEFIRQA 186

Query: 184 LETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPVHGI 243
           LETFRWHH+ATVT  QY+QLS QHRLIADVVAFKGPHINHLTPRTLDID VQA MP  GI
Sbjct: 187 LETFRWHHTATVTGAQYQQLSDQHRLIADVVAFKGPHINHLTPRTLDIDQVQAAMPGKGI 246

Query: 244 TPKAVIEGPPRRQCPILLRQTSFKALDEPVAFTDQPQAQGSHSARFGEIEQRGAALTPKG 303
           TPKAVIEGPPRR CPILLRQTSFKALDEP+AFTD   AQGSHSARFGEIEQRG ALTPKG
Sbjct: 247 TPKAVIEGPPRRHCPILLRQTSFKALDEPIAFTD---AQGSHSARFGEIEQRGVALTPKG 303

Query: 304 RALYDQLLNAARDALGAFPNEANAERYNALMTEHFVAFPDNHDELRQQALAYFRYFPTPK 363
           RALYDQLLNAARD LGAFPNE NA RY  LM  HF AFPDNH ++R+Q LAYFRYF T +
Sbjct: 304 RALYDQLLNAARDELGAFPNEGNAARYVELMERHFQAFPDNHAQMREQGLAYFRYFATEQ 363

Query: 364 GLAAKGTLEPAASLEHLLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQSNR 423
           GLAA+GT     +LE L+E  ++  EPLVYEDFLPVSAAGIFQSNLGDAAQSHYA  SNR
Sbjct: 364 GLAARGTAAQPRTLEALVEASHIDVEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAANSNR 423

Query: 424 QAFEAALGRATIDELGLYAQTQQRSIDECRAAL 456
             FE ALGR TIDEL LY +TQQRSIDEC  AL
Sbjct: 424 AEFEKALGRRTIDELKLYGETQQRSIDECTKAL 456


Lambda     K      H
   0.320    0.134    0.383 

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: 739
Number of extensions: 20
Number of successful extensions: 2
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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