Alignments for a candidate for put1 in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Pseudomonas benzenivorans DSM 8628

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_090447948.1 BLS63_RS22035 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>NCBI__GCF_900100495.1:WP_090447948.1
          Length = 1059

 Score = 1768 bits (4578), Expect = 0.0
 Identities = 887/1057 (83%), Positives = 964/1057 (91%), Gaps = 5/1057 (0%)

Query: 1    MFKAGHVLDGAFANQ----KAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRER 56
            MFKA HVL   F ++    KAA+FFP ISANYSVDEA YL+ELLQLADP EAGIAAIR  
Sbjct: 1    MFKASHVLQDEFLSRISAAKAADFFPVISANYSVDEAAYLSELLQLADPSEAGIAAIRRS 60

Query: 57   ARSLIEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLN 116
            ARSLIE VR RDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKL+
Sbjct: 61   ARSLIENVRSRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLS 120

Query: 117  AAEWERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMN 176
            AAEWERHLG+SDNVLVNFAAWGLVMTGKVVDPETADGRPKNV+G+L++RSGEPVIR AMN
Sbjct: 121  AAEWERHLGKSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVLGKLIQRSGEPVIRAAMN 180

Query: 177  QAMKLMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVE 236
            QAMKLMGKQFVLGR+I+EALKNGRP+REKGYTYSFDMLGEAALTA DA KYMADYR+A++
Sbjct: 181  QAMKLMGKQFVLGRSIAEALKNGRPQREKGYTYSFDMLGEAALTAADAEKYMADYRKAID 240

Query: 237  TVGAEPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITID 296
            TVGAEPQVG GP+PS+SIKLSALHPRYE+AQRERVLTELF +VRELAI AR+L VGI++D
Sbjct: 241  TVGAEPQVGPGPKPSISIKLSALHPRYEVAQRERVLTELFANVRELAIRARKLGVGISVD 300

Query: 297  AEEADRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPL 356
            AEEADRLELSLELYEKL+RDPAIAGWGEFGLV+QAYSKRCLPVLVWL LLG+ELG ++PL
Sbjct: 301  AEEADRLELSLELYEKLMRDPAIAGWGEFGLVVQAYSKRCLPVLVWLCLLGKELGAKMPL 360

Query: 357  RLVKGAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHN 416
            RLVKGAYWD+EIKQCQVQGLDGYPV+TRKEGTDTSYLACAR+LLSE TRGVIYPQFASHN
Sbjct: 361  RLVKGAYWDTEIKQCQVQGLDGYPVFTRKEGTDTSYLACARFLLSEFTRGVIYPQFASHN 420

Query: 417  AHTVSCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYL 476
            AHTVSCILA+A E   PREFEFQRLHGMGDALYDTV+E++ + VRIYAPVGAHKDLLPYL
Sbjct: 421  AHTVSCILAIAAEQQAPREFEFQRLHGMGDALYDTVLEQHRKTVRIYAPVGAHKDLLPYL 480

Query: 477  VRRLLENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFG-NRKNS 535
            VRRLLENGANSSFVHQLVDP  PVE+L+DHPVTQLR F   GN +IPLPPALFG  RKNS
Sbjct: 481  VRRLLENGANSSFVHQLVDPSTPVEALLDHPVTQLRAFKTLGNDKIPLPPALFGAARKNS 540

Query: 536  QGINMNIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFA 595
            QG+NMNIQ  W EL  AYQP L RQWQAAPVI G+ L+GT   VRCPY+L+K VG AQFA
Sbjct: 541  QGLNMNIQASWNELELAYQPHLNRQWQAAPVIDGQKLSGTVQPVRCPYDLSKQVGSAQFA 600

Query: 596  SADQARQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDG 655
            SA QA QA++ L   WP WNAT +++RA++LERL DLLE +RAELMALCT+EAGKSLQDG
Sbjct: 601  SAAQAAQALEVLHGAWPRWNATAIDSRASILERLADLLEANRAELMALCTLEAGKSLQDG 660

Query: 656  IDEVREAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLG 715
            IDEVREAVDFCRYYAQQARL+LGREEL+GPTGERNELFHEGRG+F CVSPWNFPLAIYLG
Sbjct: 661  IDEVREAVDFCRYYAQQARLRLGREELQGPTGERNELFHEGRGIFACVSPWNFPLAIYLG 720

Query: 716  QITAALVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPR 775
            QI AALVAGN VLAKPAEQTSLIAARALELMFEAGLP + IAFLPGDGATLGGVFCRD R
Sbjct: 721  QIAAALVAGNCVLAKPAEQTSLIAARALELMFEAGLPTDVIAFLPGDGATLGGVFCRDAR 780

Query: 776  VVGVCFTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAF 835
            V GVCFTGSTDTARIINRQLAEK GPIA LIAETGGQNAMIVDSTALPEQV+KDAV SAF
Sbjct: 781  VAGVCFTGSTDTARIINRQLAEKPGPIAALIAETGGQNAMIVDSTALPEQVVKDAVQSAF 840

Query: 836  TSAGQRCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLA 895
            TSAGQRCSALRVLYVQ DIA+RV+DLLKGAMAEL+VGPTH+R +D+GPVID EA+ GL A
Sbjct: 841  TSAGQRCSALRVLYVQADIAERVLDLLKGAMAELKVGPTHVRVSDVGPVIDAEAKAGLDA 900

Query: 896  HIQQLKSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEK 955
            HI +LK EG+LIAEA +PAGL+GHFVAPVAFEI GI +L+KE+FGPVLHVVR+ A++L++
Sbjct: 901  HIARLKGEGKLIAEAPLPAGLDGHFVAPVAFEIGGIDELQKENFGPVLHVVRFQASELDQ 960

Query: 956  VVAAINGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGT 1015
            VV AIN TGYGLTLGVHSRNEETA RIEQLARVGNLYVNRNQIGAVVGVQPFGGC LSGT
Sbjct: 961  VVGAINATGYGLTLGVHSRNEETARRIEQLARVGNLYVNRNQIGAVVGVQPFGGCGLSGT 1020

Query: 1016 GPKAGGPSYLLRFANERTTSTNTTAVGGNASLLSLGD 1052
            GPKAGGPSYLLRF NERTTS NTTAVGGNASLLSL D
Sbjct: 1021 GPKAGGPSYLLRFVNERTTSVNTTAVGGNASLLSLAD 1057


Lambda     K      H
   0.319    0.136    0.396 

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: 2919
Number of extensions: 99
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: 1053
Length of database: 1059
Length adjustment: 45
Effective length of query: 1008
Effective length of database: 1014
Effective search space:  1022112
Effective search space used:  1022112
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: 58 (26.9 bits)

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

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Candidates (tab-delimited)
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 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