GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS19355
          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.

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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:

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. 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:

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:

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