Alignments for a candidate for put1 in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Chromobacterium vaccinii MWU205

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_046158485.1 VL52_RS18890 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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



>NCBI__GCF_000971335.1:WP_046158485.1
          Length = 1197

 Score = 1446 bits (3742), Expect = 0.0
 Identities = 787/1212 (64%), Positives = 920/1212 (75%), Gaps = 33/1212 (2%)

Query: 25   SPLRAAITAAYRRDEREAVQWLLQQVQEEQPWKDATQQLARKLVQQVREKRTRSSGVDAL 84
            S LR AITAAYRRDERE VQ LL Q         + Q LAR+LV +VR +RTRSSGVDAL
Sbjct: 11   SALRDAITAAYRRDERECVQALLSQAAMSPEQVASVQDLARRLVTEVRRERTRSSGVDAL 70

Query: 85   MHEFSLSSEEGVALMCLAEALLRIPDRQTADRLIADKISKGDWRKHLGESPSLFVNAATW 144
            MHEFSL S EG+ALMCLAEALLRIPDR+TAD+LI DKIS+GDW+ HLG S SLFVNAA W
Sbjct: 71   MHEFSLDSSEGIALMCLAEALLRIPDRETADKLIRDKISRGDWKAHLGNSSSLFVNAAAW 130

Query: 145  GLLITGKLVSTSSESGLTQAITRLIGKGGEPLIRKGVDLAMRMLGNQFVTGQTIEEALDN 204
            GLL+TGKLVS+ S +GL+ A+TRLI KGGEPLIRKGVD+AMRMLG QFVTG+TIEEAL N
Sbjct: 131  GLLVTGKLVSSHSANGLSAAMTRLIAKGGEPLIRKGVDMAMRMLGKQFVTGETIEEALAN 190

Query: 205  SRENEKRGYRYSYDMLGEAALTMHDADAYYQSYESAIHAIGRASNGRGIKDGPGISVKLS 264
             RE E RGYR+SYDMLGEAA+T  DA  Y + Y +AIHAIG+ SNGRGI DGPGISVKLS
Sbjct: 191  GREREARGYRFSYDMLGEAAMTEADAQRYLKDYVTAIHAIGKESNGRGIYDGPGISVKLS 250

Query: 265  ALHPRYSRAQHARVMSELLPRLKQLLLLAKQYDIGLNIDAEEADRLELSLDMMEVLVADP 324
            A+HPRYSR +H R+M+ELLPRLK L LLAKQY+IGLNIDAEEADRLE+S+D++E L  D 
Sbjct: 251  AIHPRYSRLKHERMMAELLPRLKALFLLAKQYNIGLNIDAEEADRLEISMDLVEALANDS 310

Query: 325  DLAGFDGLGFVVQGYQKRCPFVIDYLVDLARRNGRRLMIRLVKGAYWDSEIKRAQVDGLE 384
            DL GF+G+G VVQ YQKRCPFVID L+DLARR G R M+RLVKGAYWD+EIKRAQVDGL 
Sbjct: 311  DLNGFEGIGIVVQAYQKRCPFVIDVLIDLARRTGHRFMVRLVKGAYWDAEIKRAQVDGLP 370

Query: 385  GYPVYTRKVHTDLSYLTCAQKLLAATDVIYPQFATHNAHTLAAIYHWARQHQIDNYEFQC 444
            GYPVYTRKV+TD+SYL CA+KLLAA D IYPQFATHNA++L+A+Y+ A      +YEFQC
Sbjct: 371  GYPVYTRKVYTDVSYLACAKKLLAAQDAIYPQFATHNAYSLSAVYNLAAG---KDYEFQC 427

Query: 445  LHGMGETLYDQVVGPDNLGKACRVYAPVGSHQTLLAYLVRRLLENGANSSFVNQIVDEAV 504
            LHGMGETLYDQVVG D LGKACR+YAPVGSH+TLLAYLVRRLLENGANSSFVN+IVDE+V
Sbjct: 428  LHGMGETLYDQVVGKDKLGKACRIYAPVGSHETLLAYLVRRLLENGANSSFVNRIVDESV 487

Query: 505  PLDRLVGDPIETVRAQGGLPHPAIAVPHRLYGEERKNSAGIDLSNEDRLQQLGQLFISMA 564
             LD LV DP+    A  G+PH  I++P  LYG+ R+NS G+DLS+E  L  L QL +  +
Sbjct: 488  SLDELVTDPVAEAAASAGMPHSKISLPESLYGDGRRNSKGLDLSSEHVLATL-QLGLQTS 546

Query: 565  DRQ-WQAAPLLAADTAAQSAQAAQLVRNPADLREVVGQVSEATVADVDTALRAATDYAPQ 623
            ++Q W A P+L  D      +  + VRNPAD  +VVG+V EAT ADVD AL  +   A  
Sbjct: 547  EQQRWAAFPML-GDGDVTDGELLE-VRNPADHGDVVGKVLEATAADVDRALAQSAGIAAA 604

Query: 624  WQSTPATERAAMLERAADLLEEHIAELMALAVREAGKSLPNAIAEVREAVDFLRYYA--I 681
            W +TP  ERAA + R ADL+E ++  LM LAVREAGK+L NAIAEVREAVDF RYYA  I
Sbjct: 605  WAATPVAERAASIRRMADLMEINMPALMGLAVREAGKTLNNAIAEVREAVDFCRYYAAQI 664

Query: 682  ASRHD-GNVLAWGPVVCISPWNFPLAIFIGEVSAALAAGNVVLAKPAEQTALIAHRAVQL 740
             S  D  +    GPVVCISPWNFPLAIFIGEV A+LAAGN VLAKPAEQT+LIA  A++L
Sbjct: 665  VSEFDNASHKPLGPVVCISPWNFPLAIFIGEVVASLAAGNTVLAKPAEQTSLIAAYAIRL 724

Query: 741  LHEAGIPRAALQLLPGRGETVGAALTSDVRVKGVIFTGSTEVAQLINRTLAQRQHDDGDG 800
            LHEAG+PRAALQ LPGRGE VGAALT D R++GVIFTGSTEVAQ+INRTLA + HDD   
Sbjct: 725  LHEAGVPRAALQFLPGRGEVVGAALTGDARIQGVIFTGSTEVAQIINRTLA-KHHDD--- 780

Query: 801  SGEHGEVPLIAETGGQNALIVDSSALAEQVVQDVLSSAFDSAGQRCSALRILCLQEDIAD 860
                    L+AETGG NA+IVDSSAL EQVV DVLSSAFDSAGQRCSALR+L LQ DIAD
Sbjct: 781  ------PVLVAETGGMNAMIVDSSALPEQVVTDVLSSAFDSAGQRCSALRVLYLQHDIAD 834

Query: 861  RTLAMLKGAMAELRVGRPDRLSIDIGPVIDAEARQNLLDHIERMRASARAVHQLPLGEEC 920
            + +AM+KGAM EL VG P +++ D+GPVIDAEA+  LL HI RM+ SARA+HQ  L  EC
Sbjct: 835  KVIAMIKGAMDELEVGNPAKITTDVGPVIDAEAQAGLLAHIARMKNSARAMHQTKLSAEC 894

Query: 921  QHGTFVAPTVIEIDDLAQLQREVFGPVLHVLRYRRDALPQLIDAINATGYGLTLGVHSRI 980
            + GTFVAPT+ EID+L++L+REVFGPVLHVLRY    L +++  INATGYGLT G+HSRI
Sbjct: 895  EQGTFVAPTLFEIDNLSELKREVFGPVLHVLRYAASDLDKVVAEINATGYGLTHGIHSRI 954

Query: 981  DETIEFVAQRAHVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKAGGPLYLKRLQRNAQLH 1040
            DETI  +  +  VGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKAGGP YL RL R A   
Sbjct: 955  DETIADICGKIKVGNIYVNRNIVGAVVGVQPFGGEGKSGTGPKAGGPYYLYRLTRAAWQP 1014

Query: 1041 EELTRAQPADVPNALLDSLLDWARTHGHERLAANG--QRYHRDSLLQRSLVLPGPTGERN 1098
            +     Q AD+  + LD+L   A+  G   L+ +G      ++S L  +++LPGPTGE N
Sbjct: 1015 KLAAAHQAADL--SALDALAAAAKAQG---LSLDGVIAAARKESPLAHNVILPGPTGENN 1069

Query: 1099 TLGFAPRGLVLCAAGSVGTLLNQLAAAFATGNTALV-DERSAAILPSGLPAPVRAAIRRA 1157
             L FA RG V C A     L  QLAA FA GN A+V D        S L   V      A
Sbjct: 1070 VLSFAGRGRVGCVADDAQALAEQLAAVFAAGNHAVVADGELGRRFASALNGHVSVV---A 1126

Query: 1158 SQLDAEPLQAALVDSHQAAHWRARLAAREGALVPLILCGEDTTIPLWRLLAERALCINTT 1217
              L+A+ ++A L    +    R  LAAR+GALVPLIL GE+    + RL+ ERAL +NTT
Sbjct: 1127 DVLEAD-VEAVLYAGAKVEEARRELAARDGALVPLILRGEN-GYNVHRLVVERALSVNTT 1184

Query: 1218 AAGGNASLMTIS 1229
            AAGGNASLM+++
Sbjct: 1185 AAGGNASLMSMT 1196


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: 3492
Number of extensions: 140
Number of successful extensions: 9
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: 1230
Length of database: 1197
Length adjustment: 47
Effective length of query: 1183
Effective length of database: 1150
Effective search space:  1360450
Effective search space used:  1360450
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: 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 2024 update 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