Alignments for a candidate for put1 in Xenophilus azovorans DSM 13620

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Xenophilus azovorans DSM 13620

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_038212516.1 Q392_RS22165 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::acidovorax_3H11:Ac3H11_2850
         (1261 letters)



>NCBI__GCF_000745855.1:WP_038212516.1
          Length = 1255

 Score = 1571 bits (4069), Expect = 0.0
 Identities = 827/1237 (66%), Positives = 949/1237 (76%), Gaps = 16/1237 (1%)

Query: 29   ITAATRHPEPEALAPLLAQARLPADQAAAAEQLALRIAKALRERKASAGRAGIVQGLLQE 88
            IT A R PEP+ALA LL QAR+  + A  A  LALRIA+ LRER++ AGRAGIVQGLLQE
Sbjct: 29   ITGACRMPEPQALADLLPQARMAPEAAGRAHALALRIAQGLRERRSGAGRAGIVQGLLQE 88

Query: 89   FSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISHGQWDAHLGKSPSLFVNAATWGLL 148
            ++LSSQEGVALMCLAEALLRIPD ATRDALIRDKI+HG W AH G+S SLFVNAATWGLL
Sbjct: 89   YALSSQEGVALMCLAEALLRIPDTATRDALIRDKIAHGHWQAHAGRSASLFVNAATWGLL 148

Query: 149  ITGKLVATHSEGSLGNSLSRLIGKGGEPLIRKGVDMAMRMMGEQFVTGETIDEALRNART 208
            +TGKLVATHSE SL   L+RLI +GGEP+IRKGVDMAMRMMGEQFVTGETI +AL +A+ 
Sbjct: 149  LTGKLVATHSETSLSTLLTRLIARGGEPMIRKGVDMAMRMMGEQFVTGETIQDALAHAKG 208

Query: 209  MEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQAIHAIGKASAGRGIYEGPGISIKLSALH 268
            +EA+GFRYSYDMLGEAA+T+EDA RY  SYEQAIHAIGKASAGRG+YEGPGISIKLSALH
Sbjct: 209  LEAQGFRYSYDMLGEAAMTAEDADRYRESYEQAIHAIGKASAGRGVYEGPGISIKLSALH 268

Query: 269  PRYSRAQFGRVMDELYPLVLRLTALAKQYDIGLNIDAEETDRLELSLDLLERLCHEPTLA 328
            PRYSRAQ GRVMDELYP++  L  LA ++DIGLNIDAEE DRLELSLDLL++LC EP LA
Sbjct: 269  PRYSRAQHGRVMDELYPVLRSLALLAHRHDIGLNIDAEEADRLELSLDLLDKLCFEPALA 328

Query: 329  GWNGIGFVIQAYQKRCPFVIDCVVDLARRTQRRLMVRLVKGAYWDSEIKRAQVDGLKDYP 388
            GWNGIGFVIQAYQKRCPFVID ++DLARR++ RLM+RLVKGAYWDSEIKRAQVDG   +P
Sbjct: 329  GWNGIGFVIQAYQKRCPFVIDHLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGQAGFP 388

Query: 389  VYTRKVHTDISYIACAKKLLAAPEAVYPQFATHNAETVATIYQLAG-SNYYAGQYEFQCL 447
            VYTRKV+TD+SY+ACA+KLLAAP+ VYPQFATHNA T+A IY +A  S +  GQYEFQCL
Sbjct: 389  VYTRKVYTDVSYLACARKLLAAPQQVYPQFATHNAHTMAAIYTMADPSAWQPGQYEFQCL 448

Query: 448  HGMGEPLYEQVVGAITAGKLGREIGKGGLGRPCRIYAPVGTHETLLAYLVRRLLENGANT 507
            HGMGEPLYEQVVG   AG+         LGRPCRIYAPVGTHETLLAYLVRRLLENGANT
Sbjct: 449  HGMGEPLYEQVVGPAEAGR---------LGRPCRIYAPVGTHETLLAYLVRRLLENGANT 499

Query: 508  SFVNRIADETIALDELVKSPVQVVDQQAATEGTAGLPHPRIPLPAALYGAHRSNSRGLDL 567
            SFVNR+AD TI+++ LV+ PV  V++ A  EG  G PHP I  PAALYG  R NS GLDL
Sbjct: 500  SFVNRVADPTISIETLVEDPVAAVERMAQEEGELGRPHPAIAAPAALYGEARRNSTGLDL 559

Query: 568  SNENTLTELAATLQATASHAWTAAPLLAADVPAG--TTQPVRNPADHNDVVGQVQEATTA 625
            S++ TL  L   L   A  A  A P+LA  VP      Q  RNPAD  DVVG+V+ AT  
Sbjct: 560  SDDGTLRGLETLLVQQAGTARQAEPMLAQPVPVADPAWQDKRNPADLRDVVGRVRAATEP 619

Query: 626  DVDQALVHAQAAATSWAATPPAERAAALLRTADLLEERIQPLMGLLMREAGKSASNAVAE 685
            ++D AL  A  AA +WAA P A+RAAAL RTADLL++ +  L+GLL REAGK+ +N VAE
Sbjct: 620  EIDAALRAAAEAAPAWAAMPAAQRAAALERTADLLQQALPRLLGLLAREAGKTCANGVAE 679

Query: 686  VREAVDFLRYYAAQVQSTFDNATHIPLGPVACISPWNFPLAIFMGQVAAALAAGNPVLAK 745
            VREA+DFLR+YA Q ++ FD ATH PLGPV CISPWNFPLAIF+GQ+AAALAAGN VLAK
Sbjct: 680  VREAIDFLRFYAQQARADFDAATHRPLGPVLCISPWNFPLAIFIGQIAAALAAGNTVLAK 739

Query: 746  PAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGETVGARLIGDARVMGVMFTGSTEVARI 805
            PAEQT LIAAE VRLL + GVP AA+QL+PG+G TVGAR++ DARV  VMFTGSTEVAR 
Sbjct: 740  PAEQTSLIAAEGVRLLREGGVPAAAIQLVPGRGSTVGARMVADARVQAVMFTGSTEVARQ 799

Query: 806  LQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSALVEQVVGDAVSSAFDSAGQRCSALRV 865
            LQ T+A RL + G P+PLIAETGGQNAM+VDSSALVEQVV D ++SAFDSAGQRCSALR+
Sbjct: 800  LQLTLAERLGSTGAPVPLIAETGGQNAMVVDSSALVEQVVADVMASAFDSAGQRCSALRI 859

Query: 866  LCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVGPVIDAEAQAGIAQHIEKFKAQGHRV 925
            LCVQ++ ADR++ ML+GAM E  VGNP  LR DVGPVIDA A+  I  H+E  + +G RV
Sbjct: 860  LCVQDDVADRLLHMLRGAMAEATVGNPAALRTDVGPVIDAGARETIEAHVEAMRGRGRRV 919

Query: 926  FQHPNHVSAISAPGTFVPPTLIELNHIGELQREVFGPVLHLVRYARSDLDQLLDQINATG 985
             +       +   GT+V PTLIEL  I EL+REVFGPVLH+VRYAR DLD L+ QINATG
Sbjct: 920  HRLGRCAHDVLEGGTYVVPTLIELESISELKREVFGPVLHVVRYAREDLDGLMAQINATG 979

Query: 986  YGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVGAVVGVQPFGGEGLSGTGPKAGGPLY 1045
            YGLT G+HTRIDETI +VV+RA  GN+YVNRNMVGAVVGVQPFGGEGLSGTGPKAGGPLY
Sbjct: 980  YGLTMGLHTRIDETIGQVVSRARVGNLYVNRNMVGAVVGVQPFGGEGLSGTGPKAGGPLY 1039

Query: 1046 LLRLLSQRPADALARTFAEADRTSPHDTERRERHLAPLATLQQWAHNQGNLALAGHCQRF 1105
            + RLL+ RP D LAR  A           R +      A L  WA       LA  C+  
Sbjct: 1040 MYRLLAARPGDVLARA-AGCGLPGSVPEGRAQAPSPAFAALAAWAAEHRGEGLAARCREL 1098

Query: 1106 AQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAHSVDDLLVQTAAVLASGGTALWP--H 1163
            A+   S  +R L GPTGERNVY+L PR   LCLA S D LL+Q A VLA G  A+WP   
Sbjct: 1099 ARRAGSRQARVLAGPTGERNVYSLHPREAALCLAASEDALLLQLAGVLAVGCRAIWPLTA 1158

Query: 1164 AHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHHGDAPSLQAVCTTLARRPGPIVGV 1223
            A   L A LP  VQ  + L  +  + G VA D  LH G    L+A    LA R GPIV +
Sbjct: 1159 ATGKLHAGLPLEVQGAIALASDWNAPG-VAFDVALHQGSEADLRAAAARLAERDGPIVCL 1217

Query: 1224 TALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260
                PG+ D+PLE L++ERA+S NTAAAGGNASLMTI
Sbjct: 1218 RRFDPGSDDMPLEALVLERAVSTNTAAAGGNASLMTI 1254


Lambda     K      H
   0.318    0.133    0.387 

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: 3914
Number of extensions: 173
Number of successful extensions: 6
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: 1261
Length of database: 1255
Length adjustment: 48
Effective length of query: 1213
Effective length of database: 1207
Effective search space:  1464091
Effective search space used:  1464091
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 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