Alignments for a candidate for put1 in Burkholderia vietnamiensis G4

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Burkholderia vietnamiensis G4

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011882823.1 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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



>NCBI__GCF_000016205.1:WP_011882823.1
          Length = 1309

 Score = 1752 bits (4537), Expect = 0.0
 Identities = 928/1345 (68%), Positives = 1056/1345 (78%), Gaps = 48/1345 (3%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RLK  A  ++RTPHWLIKQAIF YLE++E G +P E S    GS
Sbjct: 1    MASTTLGVKVDDLLRSRLKDAATRLERTPHWLIKQAIFAYLERIEHGQLPPELS----GS 56

Query: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120
             G  + AD       D +  PFLEFAQ+VQPQSVLRAAITAAYRRPE ECVP LL QARL
Sbjct: 57   SGVTELADGHAAEDDDNSPHPFLEFAQNVQPQSVLRAAITAAYRRPEPECVPFLLGQARL 116

Query: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180
            P         +A  L   LRE+  G G    V+GLI EFSLSSQEGVALMCLAEALLRIP
Sbjct: 117  PANLQADVQTLATHLVETLREKSSGGG----VEGLIHEFSLSSQEGVALMCLAEALLRIP 172

Query: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240
            D+ATRDALIRDKIS  +W+SH+G +PS+FVNAATWGL+ TGKLV T++EAGLS ALTR+I
Sbjct: 173  DRATRDALIRDKISKGDWRSHVGHAPSLFVNAATWGLMITGKLVTTNSEAGLSSALTRLI 232

Query: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300
            G+GGEPLIRKGVDMAMRLMGEQFVTGETISEALAN+RKYEA GFRYSYDMLGEAA TE D
Sbjct: 233  GRGGEPLIRKGVDMAMRLMGEQFVTGETISEALANSRKYEARGFRYSYDMLGEAATTEED 292

Query: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360
            A RY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALH RYSR+Q +R + EL  R+++L
Sbjct: 293  ALRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHARYSRSQQDRTMSELLPRVRAL 352

Query: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420
             LLAR+YDIG+NIDAEEADRLE+SLDLLE LCF+P+LAGWNGIGFVVQGYQKRCPFVIDY
Sbjct: 353  ALLARRYDIGLNIDAEEADRLELSLDLLEALCFDPDLAGWNGIGFVVQGYQKRCPFVIDY 412

Query: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480
            LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+KLL+ 
Sbjct: 413  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKKLLAA 472

Query: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540
            PD +YPQFATHNA+TLAAIY +AG NYYPGQYEFQCLHGMGEPLY++V G     K NRP
Sbjct: 473  PDAVYPQFATHNAYTLAAIYHLAGQNYYPGQYEFQCLHGMGEPLYEEVTG---RDKLNRP 529

Query: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600
            CR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD T+S+ ELVADPV    ++     
Sbjct: 530  CRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADKTVSVKELVADPVDEASKV----V 585

Query: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660
             LG PH +I  PR LYG+ RANS G+DLSNEHRLASLSSALLA       A P+L  +A 
Sbjct: 586  PLGAPHAKIPLPRNLYGDERANSMGLDLSNEHRLASLSSALLASAHHPWRAAPMLADDAL 645

Query: 661  AGEDVNQPA-PVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALE 719
            A    + PA  VRNP+DQRDVVG V+EA+   V AAL  AV AAPIWQATP D RA  L 
Sbjct: 646  A----DAPARDVRNPADQRDVVGAVSEATSEHVSAALAHAVAAAPIWQATPVDARADCLV 701

Query: 720  RAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGP 779
            RAA+L+EAQM +LMG+IVREAGK+  NAIAE+REAVDFLRYYAAQ+R  FS+DTHRPLGP
Sbjct: 702  RAADLLEAQMHTLMGLIVREAGKSLPNAIAEIREAVDFLRYYAAQIRGEFSNDTHRPLGP 761

Query: 780  VVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLL 839
            VVCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLL
Sbjct: 762  VVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLL 821

Query: 840  PGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMI 899
            PG GETVGAALV D R + VMFTGSTEVARL+ ++++ RLD  G+P+PLIAETGGQNAMI
Sbjct: 822  PGTGETVGAALVADPRTRAVMFTGSTEVARLINKTLSARLDPDGKPIPLIAETGGQNAMI 881

Query: 900  VDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDR 959
            VDSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR L MLKGAM EL +GNPDR
Sbjct: 882  VDSSALAEQVVADVMQSSFDSAGQRCSALRVLCLQDDVADRTLTMLKGAMHELALGNPDR 941

Query: 960  LSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIELDSI 1019
            LSTDVGPVID EA+  I  H+ AM+ KG  V Q      +  AC +GTFV PTLIE+ SI
Sbjct: 942  LSTDVGPVIDAEAKQTIDTHVAAMKDKGHAVTQL----PMPDACAHGTFVPPTLIEIGSI 997

Query: 1020 EELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNL 1079
            +EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++  A VGN+
Sbjct: 998  DELKREVFGPVLHVVRYRRSQLDKLLEQIRATGYGLTLGIHTRIDETIAHVIANAHVGNI 1057

Query: 1080 YVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPL---DAVARVVRASDTVG 1136
            YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P     A+A+ + A     
Sbjct: 1058 YVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPSGLPKALAQTLIADGVAE 1117

Query: 1137 GADETGPVRRTLTETLATLKEW--AQRESAALPGLVAACERFAAASAAGLSVTLPGPTGE 1194
            G     P        L  L++W   QRE    P L A C+ + +   AG +  L GPTGE
Sbjct: 1118 GEQRGNP-----AAALTALRDWLIEQRE----PALAARCDGYLSQVPAGATAVLTGPTGE 1168

Query: 1195 RNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVR 1254
            RNTYTL PR  VLC+A   +    Q AAVLA G++A++  S    AL A LP A++    
Sbjct: 1169 RNTYTLGPRGTVLCVAATPSGARAQFAAVLATGNRALFAGS-AGEALVAALPAALKGH-- 1225

Query: 1255 LVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLAHG------EPNIAIE 1308
              A     D  FDAVL  GDSD+L+ + + +A RPGPI+SVQG++ G        + A+E
Sbjct: 1226 -AAVRKQADAPFDAVLFEGDSDELQTLVKDVAQRPGPIVSVQGVSAGAFENGDAEDYALE 1284

Query: 1309 RLLIERSLSVNTAAAGGNASLMTIG 1333
            RLL ERS+SVNTAAAGGNA+LMTIG
Sbjct: 1285 RLLTERSVSVNTAAAGGNANLMTIG 1309


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: 4138
Number of extensions: 172
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: 1309
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1260
Effective search space:  1617840
Effective search space used:  1617840
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