Alignments for a candidate for put1 in Paraburkholderia sp. CCGE1002

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Paraburkholderia sp. CCGE1002

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_013090943.1 BC1002_RS15505 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>NCBI__GCF_000092885.1:WP_013090943.1
          Length = 1312

 Score = 1754 bits (4544), Expect = 0.0
 Identities = 926/1350 (68%), Positives = 1063/1350 (78%), Gaps = 55/1350 (4%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RLK  A  ++RTPHWLIKQAIF YLE++E G +P E S      
Sbjct: 1    MASTTLGVKVDDLLRSRLKDAATRLERTPHWLIKQAIFAYLEKIEHGQLPAELS------ 54

Query: 61   EGAADGADAFDGAA----SDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLE 116
             GAA  AD  DGAA     DGA  PFL+FAQ+VQPQSVLRAAITAAYRRPE ECVP LL 
Sbjct: 55   -GAAGTADLADGAAVENEEDGASHPFLDFAQNVQPQSVLRAAITAAYRRPEPECVPFLLG 113

Query: 117  QARLPHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEAL 176
            QARLP   A    AMA  L   LR +  G G    V+GLI EFSLSSQEGVALMCLAEAL
Sbjct: 114  QARLPANLAGDVQAMAGKLVETLRTKSKGGG----VEGLIHEFSLSSQEGVALMCLAEAL 169

Query: 177  LRIPDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKAL 236
            LRIPD+ATRDALIRDKIS  +W+SH+GQ+PS+FVNAATWGL+ TGKLV T++E  LS AL
Sbjct: 170  LRIPDRATRDALIRDKISKGDWKSHVGQAPSLFVNAATWGLMITGKLVTTNSETSLSSAL 229

Query: 237  TRIIGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAM 296
            TR+IGKGGEPLIRKGVDMAMRLMGEQFVTGE ISEALAN+RKYEA GFRYSYDMLGEAA 
Sbjct: 230  TRLIGKGGEPLIRKGVDMAMRLMGEQFVTGENISEALANSRKYEARGFRYSYDMLGEAAT 289

Query: 297  TEADAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGR 356
            TEADAQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALHPRYSRAQ ER + EL  R
Sbjct: 290  TEADAQRYFASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHPRYSRAQQERTMSELLPR 349

Query: 357  LKSLTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPF 416
            ++SL +LAR+YDIG+NIDAEEADRLE+SLDLLE LCF+PEL GWNGIGFVVQ YQKRCPF
Sbjct: 350  VRSLAILARRYDIGLNIDAEEADRLELSLDLLEALCFDPELQGWNGIGFVVQAYQKRCPF 409

Query: 417  VIDYLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARK 476
            VIDY++DLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRKVYTDVSY+ACA+K
Sbjct: 410  VIDYIVDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKVYTDVSYLACAKK 469

Query: 477  LLSVPDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGK 536
            LL  PD +YPQFATHNAHTL+AIY +AG+NYYPGQYEFQCLHGMGEPLY++V G     K
Sbjct: 470  LLGAPDAVYPQFATHNAHTLSAIYHLAGNNYYPGQYEFQCLHGMGEPLYEEVTG---RDK 526

Query: 537  FNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMH 596
             NRPCR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+++++ +LVADPV    ++ 
Sbjct: 527  LNRPCRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADESVAIKDLVADPVEEASKI- 585

Query: 597  ADEGALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLG 656
                 LG PH RI  PR LYG  R NS G+DLSNEHRLASLSSALLA       A P+L 
Sbjct: 586  ---VPLGAPHARIPLPRNLYGAERLNSMGLDLSNEHRLASLSSALLASAHHPWRAAPMLE 642

Query: 657  TEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAA 716
                A   V     VRNP+DQRD+VG V EA+   V AAL  AV AAPIWQATP + RA 
Sbjct: 643  DNQIA---VGAGRDVRNPADQRDLVGTVVEATPEHVSAALGHAVAAAPIWQATPVEARAD 699

Query: 717  ALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRP 776
             L RAA+L+EAQM +LMG++VREAGK+ +NA+AE+REA+DFLRYY+AQ+R+ FS+DTHRP
Sbjct: 700  CLARAADLLEAQMHTLMGLVVREAGKSLANAVAEIREAIDFLRYYSAQIRDEFSNDTHRP 759

Query: 777  LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAV 836
            LGPVVCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAGAV
Sbjct: 760  LGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAGAV 819

Query: 837  QLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQN 896
            QLLPG GETVGAALV D R + VMFTGSTEVARL+ ++++GRLD  G+P+PLIAETGGQN
Sbjct: 820  QLLPGNGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPDGKPIPLIAETGGQN 879

Query: 897  AMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGN 956
            AMIVDSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ+++ADR LEML GAM EL +GN
Sbjct: 880  AMIVDSSALAEQVVADVLQSSFDSAGQRCSALRVLCLQDDIADRTLEMLTGAMRELALGN 939

Query: 957  PDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQAD-PNGALSAACRNGTFVSPTLIE 1015
            PDRLSTDVGPVID +A+  I  HI AMR KGR+V Q   P GA       GTFV PTLIE
Sbjct: 940  PDRLSTDVGPVIDLDAKRGIDAHIAAMRDKGRKVEQLPLPEGA-----TQGTFVPPTLIE 994

Query: 1016 LDSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAE 1075
            LDSI+EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++  A 
Sbjct: 995  LDSIDELKREVFGPVLHVVRYRRSQLDKLLEQIRATGYGLTLGIHTRIDETIAHVISHAH 1054

Query: 1076 VGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLD-----AVARVVR 1130
            VGN+YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P       A A VV 
Sbjct: 1055 VGNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLAKRPAGLPKSLAQALVVE 1114

Query: 1131 ASDTVGGADETGPVRRTLTETLATLKEW--AQRESAALPGLVAACERFAAASAAGLSVTL 1188
                   A++ G     LT     L++W  A+RE    P L A C+ + +   AG +  L
Sbjct: 1115 VPQAAQAAEKGGNPAAALT----ALRDWLIAERE----PQLAARCDGYLSHVPAGATAVL 1166

Query: 1189 PGPTGERNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKA 1248
             GPTGERNTYTL PR  VLC+A   +   VQ AA LA G++A++ E      L ++LP +
Sbjct: 1167 SGPTGERNTYTLGPRGTVLCIASTASGARVQFAAALATGNRALF-EGAAGEQLVSQLPAS 1225

Query: 1249 VQSRVRLVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQG-----LAHGEP 1303
            +++   +     + D  FDAVL  GDSD+L  + +++A R GPI+SVQG     LA G+ 
Sbjct: 1226 LKAHASVK---KSADAPFDAVLFEGDSDELLTLVKEVAKRAGPIVSVQGVAARALASGDE 1282

Query: 1304 NIAIERLLIERSLSVNTAAAGGNASLMTIG 1333
            + A+ERLL ERS+SVNTAAAGGNA+LMTIG
Sbjct: 1283 DYALERLLTERSVSVNTAAAGGNANLMTIG 1312


Lambda     K      H
   0.318    0.133    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: 4007
Number of extensions: 154
Number of successful extensions: 11
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: 1333
Length of database: 1312
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1263
Effective search space:  1621692
Effective search space used:  1621692
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