GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hglS in Pseudomonas fluorescens FW300-N2E3

Align putative hydrolase, required for lysine catabolism (characterized)
to candidate AO353_21295 AO353_21295 hypothetical protein

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21295 AO353_21295
           hypothetical protein
          Length = 465

 Score =  727 bits (1877), Expect = 0.0
 Identities = 372/455 (81%), Positives = 403/455 (88%)

Query: 4   VSPDLIRQRFSRAMSDMYRDEVPLYGALMKLVEHTNAQVLSEQPQLAEHLRSTGELERLD 63
           VSPDLIRQRFSRAMSDMYR+EVPLYGALM+LV  TN QVL   P +A  LRSTGE+ERLD
Sbjct: 7   VSPDLIRQRFSRAMSDMYREEVPLYGALMELVAQTNVQVLDSDPAIARQLRSTGEIERLD 66

Query: 64  LERHGAIRVGTAAELATLGRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHESALQVSPF 123
           LERHGAIRVGTA ELATL RLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHE++LQVSPF
Sbjct: 67  LERHGAIRVGTAQELATLCRLFAVMGMQPVGYYDLTPAGVPVHSTAFRAVHEASLQVSPF 126

Query: 124 RVFTSLLRLELIENSELRAFAESVLAKRQIFTPGALALIDLAERQGGLTQAQAEDFVLQA 183
           RVFTSLLRLELIEN ELRAFAESVLAKR IFT  AL LI+ AE+ GGL + QAEDFV QA
Sbjct: 127 RVFTSLLRLELIENPELRAFAESVLAKRSIFTAQALKLIEQAEQHGGLDEQQAEDFVEQA 186

Query: 184 LETFRWHHSATVTAEQYRQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQARMPVHGI 243
           LETFRWHH ATVTA QY+QLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQA+MP +GI
Sbjct: 187 LETFRWHHRATVTAAQYQQLSAQHRLIADVVAFKGPHINHLTPRTLDIDIVQAKMPEYGI 246

Query: 244 TPKAVIEGPPRRQCPILLRQTSFKALDEPVAFTDQPQAQGSHSARFGEIEQRGAALTPKG 303
           TPKAVIEGPPRRQCPILLRQTSFKALDEP+AFTDQ QA GSHSARFGEIEQRGAALTP+G
Sbjct: 247 TPKAVIEGPPRRQCPILLRQTSFKALDEPIAFTDQQQALGSHSARFGEIEQRGAALTPEG 306

Query: 304 RALYDQLLNAARDALGAFPNEANAERYNALMTEHFVAFPDNHDELRQQALAYFRYFPTPK 363
           RALYD+LLNAARDAL  FPNEANA RY++LM +HF AFPD+++E+R+Q LAYFRYF T K
Sbjct: 307 RALYDRLLNAARDALNDFPNEANAARYHSLMEQHFKAFPDSYNEMREQGLAYFRYFVTEK 366

Query: 364 GLAAKGTLEPAASLEHLLEQQYLRAEPLVYEDFLPVSAAGIFQSNLGDAAQSHYAGQSNR 423
           GLAA      +ASL  LL+ +Y+RA PLVYEDFLPVSAAGIFQSNLGDAAQ+HY   SNR
Sbjct: 367 GLAADSDELGSASLRGLLDAEYIRAVPLVYEDFLPVSAAGIFQSNLGDAAQTHYGEHSNR 426

Query: 424 QAFEAALGRATIDELGLYAQTQQRSIDECRAALGV 458
           QAFE ALGR+TIDEL LYA TQ+RSI+EC AAL V
Sbjct: 427 QAFEQALGRSTIDELALYADTQRRSIEECCAALNV 461


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: 778
Number of extensions: 18
Number of successful extensions: 1
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: 465
Length adjustment: 33
Effective length of query: 425
Effective length of database: 432
Effective search space:   183600
Effective search space used:   183600
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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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 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