Alignments for a candidate for put1 in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Dyella japonica UNC79MFTsu3.2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Query= reanno::HerbieS:HSERO_RS00905
         (1230 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4232
          Length = 1074

 Score = 1081 bits (2795), Expect = 0.0
 Identities = 591/1047 (56%), Positives = 723/1047 (69%), Gaps = 37/1047 (3%)

Query: 21   LPTPS-PLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDATQQLARKLVQQVREKRTRSS 79
            LPT + P RA ITAA+ RDE EAV  LL Q       ++    LA  LV +VR +    S
Sbjct: 33   LPTGAEPARARITAAWLRDETEAVNDLLVQASLPPVEREKVIDLAADLVTRVRARAKDQS 92

Query: 80   GVDALMHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHLGESPSLFV 139
             V++ M ++ LSSEEGV LMC+AEALLRIPD+ TAD+LI DK+   +W+KHLG+S SLFV
Sbjct: 93   AVESFMRQYDLSSEEGVLLMCVAEALLRIPDKATADKLIRDKLGDANWKKHLGQSESLFV 152

Query: 140  NAATWGLLITGKLVSTSSE--SGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQFVTGQT 197
            NA+TWGL++TGKLV+ + +     T A+ RL+G+ GEP IR  V  AMR++G+QFV G+T
Sbjct: 153  NASTWGLMLTGKLVNLAGDIRHDFTGALRRLVGRAGEPAIRLAVRQAMRIMGHQFVMGRT 212

Query: 198  IEEALDNSRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGRGIKDGP 257
            I EALD   + E   YRYSYDMLGE+ALT   A+ Y Q Y +AI AIG         D P
Sbjct: 213  IGEALDRCAQKEYAVYRYSYDMLGESALTSETAERYQQDYRNAIAAIGARGPFANHTDAP 272

Query: 258  GISVKLSALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLELSLDMM 317
             ISVKLSALHPRY  A+      +L  +L +L  LA ++ I L++DAEEADRLELSLD++
Sbjct: 273  SISVKLSALHPRYEVAKRELARRDLTAKLLELSQLAMKHGIALSVDAEEADRLELSLDIL 332

Query: 318  EVLVADPDLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYWDSEIKR 377
              + A P LAG++GLG VVQ Y KR PFVID+L++ AR +GRR  +RLVKGAYWD+E+KR
Sbjct: 333  GDVFAHPSLAGWNGLGIVVQAYSKRTPFVIDWLIETARGSGRRWYVRLVKGAYWDAEVKR 392

Query: 378  AQVDGLEGYPVYTRKVHTDLSYLTCAQKLL-AATDVIYPQFATHNAHTLAAIYHWARQHQ 436
            AQ +GL GYPVYTRK +TD+SYL CA+KL  A  ++IYPQFATHNAHT+AA++H A+   
Sbjct: 393  AQENGLPGYPVYTRKPNTDVSYLACARKLFDAGIELIYPQFATHNAHTIAAVHHLAKGRP 452

Query: 437  IDNYEFQCLHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLLENGANSSFV 496
               YE+Q LHGMG  LY +V+G  NL   CRVYAPVG+H+ LL YLVRRLLENGAN+SFV
Sbjct: 453  ---YEYQRLHGMGTDLYAEVIGAQNLNVPCRVYAPVGTHEDLLPYLVRRLLENGANTSFV 509

Query: 497  NQIVDEAVPLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDLSNEDRLQQL 556
            N++VDE++P+  LV DP ETVR+   +PHP I +P  LYGE RKNS G++ SN++ L+ L
Sbjct: 510  NRVVDESLPVRELVADPCETVRSFASIPHPRIPLPVNLYGELRKNSMGVNFSNDNELKAL 569

Query: 557  GQLFISMADRQWQAAPLLAADTAAQSAQAAQLVRNPADLREVVGQVSEATVADVDTALRA 616
             +  ++     W A PL+     A SA A   V NPAD R+VVG    A  A V+ AL  
Sbjct: 570  AET-VNAKSGPWTATPLV---PGATSAGATVQVTNPADRRQVVGSYVSADSATVEKALAN 625

Query: 617  ATDYAPQWQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNAIAEVREAVDFL 676
            A      W   PA  RAA+LE AA+ LE    E +AL VREAGK LP+AIAE+REA DFL
Sbjct: 626  AVAAQHGWDRLPAASRAAILEHAAEQLEARRGEFIALCVREAGKGLPDAIAEIREAADFL 685

Query: 677  RYYAIASRH-------------DGNVL---AWGPVVCISPWNFPLAIFIGEVSAALAAGN 720
            RYYA  +R              + N L     G  VCISPWNFPLAIF+G+V+AALAAGN
Sbjct: 686  RYYATMARRYFGQPEQLPGPTGESNQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGN 745

Query: 721  VVLAKPAEQTALIAHRAVQLLHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGST 780
             V+AKPAEQT+LI H AVQLLHEAG+P   LQ LPG G TVGAALT D RV GV FTGST
Sbjct: 746  SVIAKPAEQTSLIGHAAVQLLHEAGVPADVLQYLPGDGATVGAALTRDPRVAGVAFTGST 805

Query: 781  EVAQLINRTLAQRQHDDGDGSGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFD 840
            E A  INR LA R               LIAETGGQNA+I DSSAL EQ+V+D +SSAF 
Sbjct: 806  ETAWAINRALAARNAP---------IAALIAETGGQNAMIADSSALPEQIVKDAVSSAFQ 856

Query: 841  SAGQRCSALRILCLQEDIADRTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDH 900
            SAGQRCSA R+L +QEDIAD+  AML GAMAEL+VG P +LS D+GPVID +AR+ L+DH
Sbjct: 857  SAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKVGDPAQLSTDVGPVIDEDARKILVDH 916

Query: 901  IERMRASARAVHQLPLGEECQ-HGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALP 959
              RM   A+ + ++ L      +GTF AP   EI  LA L RE+FGPVLHV+R++   L 
Sbjct: 917  AARMDQEAKKIGEVALDPATTGNGTFFAPRAYEIPGLATLTREIFGPVLHVIRWKGSELD 976

Query: 960  QLIDAINATGYGLTLGVHSRIDETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSG 1019
            +++D INATGYGLTLG+HSRID+T+EF+  RA VGN YVNRN +GAVVGVQPFGGEG SG
Sbjct: 977  KVVDEINATGYGLTLGIHSRIDDTVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSG 1036

Query: 1020 TGPKAGGPLYLKRLQRNAQLHEELTRA 1046
            TGPKAGGP YL R      L    T A
Sbjct: 1037 TGPKAGGPHYLFRFAGERTLTINTTAA 1063



 Score = 40.0 bits (92), Expect = 1e-06
 Identities = 40/126 (31%), Positives = 54/126 (42%), Gaps = 23/126 (18%)

Query: 1090 LPGPTGERNTLGFAPRGLVLCAAG---SVGTLLNQLAAAFATGN---------TALVDER 1137
            LPGPTGE N L    RG+ +C +     +   L Q+AAA A GN         T+L+   
Sbjct: 702  LPGPTGESNQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHA 761

Query: 1138 SAAIL-PSGLPAPV-------RAAIRRASQLDAEPLQAALVDSHQAAHW--RARLAAREG 1187
            +  +L  +G+PA V        A +  A   D      A   S + A W     LAAR  
Sbjct: 762  AVQLLHEAGVPADVLQYLPGDGATVGAALTRDPRVAGVAFTGSTETA-WAINRALAARNA 820

Query: 1188 ALVPLI 1193
             +  LI
Sbjct: 821  PIAALI 826



 Score = 39.7 bits (91), Expect = 1e-06
 Identities = 19/26 (73%), Positives = 21/26 (80%)

Query: 1203 LWRLLAERALCINTTAAGGNASLMTI 1228
            L+R   ER L INTTAAGGNASL+TI
Sbjct: 1047 LFRFAGERTLTINTTAAGGNASLLTI 1072


Lambda     K      H
   0.319    0.134    0.389 

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: 2993
Number of extensions: 145
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 1230
Length of database: 1074
Length adjustment: 46
Effective length of query: 1184
Effective length of database: 1028
Effective search space:  1217152
Effective search space used:  1217152
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 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:

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