GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Burkholderia phytofirmans PsJN

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate BPHYT_RS19355 BPHYT_RS19355 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

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



>lcl|FitnessBrowser__BFirm:BPHYT_RS19355 BPHYT_RS19355 bifunctional
            proline dehydrogenase/pyrroline-5-carboxylate
            dehydrogenase
          Length = 1309

 Score = 1751 bits (4534), Expect = 0.0
 Identities = 916/1339 (68%), Positives = 1054/1339 (78%), Gaps = 36/1339 (2%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RLK  A  ++RTPHWLIKQAIF YLE++E G +P E S   TGS
Sbjct: 1    MASTTLGVKVDDLLRSRLKDAATRLERTPHWLIKQAIFAYLEKIEHGQLPPELSGV-TGS 59

Query: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120
               ADGA        DGA  PFLEFAQ+VQPQSVLRAAITAAYRRPE EC+P L+ QARL
Sbjct: 60   ADLADGASVEQ--EEDGASHPFLEFAQNVQPQSVLRAAITAAYRRPEPECLPFLVGQARL 117

Query: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180
            P   A     MA  L   LR +  G G    V+GLI EFSLSSQEGVALMCLAEALLRIP
Sbjct: 118  PANLAGDVQTMAGKLVETLRTKSKGGG----VEGLIHEFSLSSQEGVALMCLAEALLRIP 173

Query: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240
            D+ATRDALIRDKIS  +W+SH+GQ+PS+FVNAATWGL+ TGKLV T++E  LS ALTR+I
Sbjct: 174  DRATRDALIRDKISKGDWKSHMGQAPSMFVNAATWGLMITGKLVTTNSETSLSSALTRLI 233

Query: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300
            GKGGEPLIRKGVDMAMRLMGEQFVTGE ISEALAN+RKYEA GFRYSYDMLGEAA TEAD
Sbjct: 234  GKGGEPLIRKGVDMAMRLMGEQFVTGENISEALANSRKYEARGFRYSYDMLGEAATTEAD 293

Query: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360
            AQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALH RYSR+Q ER + EL  R++SL
Sbjct: 294  AQRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHARYSRSQQERTMSELLPRVRSL 353

Query: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420
             +LAR+YDIG+NIDAEEADRLEISLDLLE LCF+PELAGWNGIGFVVQ YQKRCPFVIDY
Sbjct: 354  AILARRYDIGLNIDAEEADRLEISLDLLEALCFDPELAGWNGIGFVVQAYQKRCPFVIDY 413

Query: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480
            +IDLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+KLLS 
Sbjct: 414  IIDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKKLLSA 473

Query: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540
            PD +YPQFATHNAHTL+AIY +AG+NYYPGQYEFQCLHGMGEPLY++V G     K NRP
Sbjct: 474  PDAVYPQFATHNAHTLSAIYHLAGNNYYPGQYEFQCLHGMGEPLYEEVTG---RDKLNRP 530

Query: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600
            CR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+ +++ +L+ADPV    ++     
Sbjct: 531  CRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADENVAIKDLIADPVDEASKI----V 586

Query: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660
             LG PH +I  PR LYG  R NS G+DLSNEHRLASLSSALLA       A P+L     
Sbjct: 587  PLGAPHAKIPLPRNLYGAERLNSMGLDLSNEHRLASLSSALLASAHHPWRAAPMLEDNEI 646

Query: 661  AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER 720
            A   V     VRNP+D RD+VG V EA+   V AAL  AV AAPIWQATP D RA  L R
Sbjct: 647  A---VGVARDVRNPADHRDLVGTVVEATPEHVSAALAHAVAAAPIWQATPVDARADCLAR 703

Query: 721  AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV 780
            AA+L+EAQM +LMG++VREAGK+ +NA+AE+REA+DFLRYY+ Q+R+ FS+DTHRPLGPV
Sbjct: 704  AADLLEAQMHTLMGLVVREAGKSLANAVAEIREAIDFLRYYSTQIRDEFSNDTHRPLGPV 763

Query: 781  VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP 840
            VCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAGAVQLLP
Sbjct: 764  VCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAGAVQLLP 823

Query: 841  GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV 900
            G GETVGAALV D R + VMFTGSTEVARL+ ++++GRLD  G+P+PLIAETGGQNAMIV
Sbjct: 824  GNGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPDGKPIPLIAETGGQNAMIV 883

Query: 901  DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL 960
            DSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR LEML GAM EL +GNPDRL
Sbjct: 884  DSSALAEQVVADVLQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMRELAVGNPDRL 943

Query: 961  STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQAD-PNGALSAACRNGTFVSPTLIELDSI 1019
            S DVGPVID +A+  I  H+  MR KGR+V Q   P+G     C  GTFV PTLIELDSI
Sbjct: 944  SIDVGPVIDLDAKRGIDAHVATMREKGRKVEQLPMPDG-----CAQGTFVPPTLIELDSI 998

Query: 1020 EELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNL 1079
            +EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++ RA VGN+
Sbjct: 999  DELKREVFGPVLHVVRYRRSQLDKLLEQIRTTGYGLTLGIHTRIDETIAHVISRAHVGNI 1058

Query: 1080 YVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGAD 1139
            YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P      + +A   V  A 
Sbjct: 1059 YVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPAGLPKSLAQA--LVADAP 1116

Query: 1140 ETGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYT 1199
                     +  L   ++W   E    P L A C+ + +   AG +  L GPTGERNTYT
Sbjct: 1117 NAAENSDNPSAALTAYRDWLIAEQQ--PVLAARCDGYLSHMPAGATAVLSGPTGERNTYT 1174

Query: 1200 LLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADW 1259
            L PR  VLC+A   +   VQ AA LA G++A++ E      L A+LP +++SR  +    
Sbjct: 1175 LGPRGTVLCIASTASGARVQFAAALATGNRALF-EGAAGEQLVAQLPASLKSRASVK--- 1230

Query: 1260 SAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLA-----HGEPNIAIERLLIER 1314
             + D  FDAVL  GDSD+L A+ +++A RPGPI+SVQG+A      G+ + A+ERLL ER
Sbjct: 1231 KSADATFDAVLFEGDSDELLALVKEVAKRPGPIVSVQGVAARALESGDEDYALERLLTER 1290

Query: 1315 SLSVNTAAAGGNASLMTIG 1333
            S+SVNTAAAGGNA+LMTIG
Sbjct: 1291 SVSVNTAAAGGNANLMTIG 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: 3982
Number of extensions: 147
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, or view the source code.

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