GapMind for catabolism of small carbon sources

 

Alignments for a candidate for odc in Magnetospirillum magneticum AMB-1

Align ornithine decarboxylase (EC 4.1.1.17) (characterized)
to candidate WP_011383521.1 AMB_RS05630 amino acid decarboxylase

Query= BRENDA::A4Q8H0
         (720 letters)



>NCBI__GCF_000009985.1:WP_011383521.1
          Length = 783

 Score =  592 bits (1525), Expect = e-173
 Identities = 308/706 (43%), Positives = 431/706 (61%), Gaps = 32/706 (4%)

Query: 44  AKGMVTHLEEIGLNIPLFVAVCCE--EELDNAVLPALHGVFELCGKNTQFYGKQLEAAAV 101
           A  ++  +   GL +P+ + V  E  E++   VL  + G   L  +  +F  K L +   
Sbjct: 75  ATELINLMRRRGLEMPIVILVRGERFEDIPVDVLDYIDGYVFLAEETPEFIAKNLVSRLK 134

Query: 102 KYEKDLLPPFFNTLTQYVEMGNATFACPGHQGGEFFRKHPAGRQFFDFYGETLFRSDMCN 161
           ++ + L  PFF  L  Y E GN  + CPGH GG F+ + P GR F +  GE +FR D+ N
Sbjct: 135 QFAETLKTPFFGALVDYAEEGNQLWTCPGHNGGIFYNRSPIGRIFVEHLGEAVFRDDLDN 194

Query: 162 ADVKLGDLLIHEGLPCAAQQHAAKVFNADKTYFVLNGTSASNKVATNALLTRGDLVLFDR 221
           + ++LGDLL HEG    AQ+ AAK+F A+KTYFVLNGTSASNK+  +AL+   DLVLFDR
Sbjct: 195 SVLELGDLLTHEGPALQAQKEAAKIFGAEKTYFVLNGTSASNKIVLSALVAEDDLVLFDR 254

Query: 222 NNHKSNHHGALIQAGATPVYLETARNPFGFIGGIDAHCFDERYLRQQIRE----VAPERA 277
           NNHK+ HHGAL+  G  P++LET RN  G IG I A  FDE+ +R +IR+      PE  
Sbjct: 255 NNHKAAHHGALLLGGGIPIFLETDRNAMGMIGPIYAEAFDEQAIRAKIRDNPLVKDPEAW 314

Query: 278 NEARPFRLAIIQLGTYDGTIYNARQVVDKIGHLCDYILFDSAWVGYEQFIPMMKDCSPLL 337
            + RPFR+A+I+  TYDGTIY+A  ++++IGHLCDYILFD AW G+ +F P+ + C  + 
Sbjct: 315 KKPRPFRVAVIEQCTYDGTIYSAEHILERIGHLCDYILFDEAWAGFLKFHPLFRGCYGMG 374

Query: 338 LE--LNENDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQSRYCNHKRFNNAFMLHAST 395
           L+  L+E+ PGII TQS HKQ AGFSQ SQIH +D+HIKGQSR   H+RFN  F+LHAST
Sbjct: 375 LKDRLDEDSPGIISTQSTHKQMAGFSQASQIHVRDRHIKGQSRRIEHRRFNETFLLHAST 434

Query: 396 SPFYPLFAALDVNAKMHEGKSGQRLWKECVRVGIEARKMLLETCQ-------------LI 442
           SPFYPLFA+LDV A+M  G+SG+ LW + + +GIE RK +    +               
Sbjct: 435 SPFYPLFASLDVGAQMMRGRSGEVLWDDTIDLGIELRKKVRAIKREFVEKEKDSARHWFF 494

Query: 443 KPFVPDQIDGK-------PWQSYDTETMANDLRFFNFVPGEKWHAFEGYAESQY-FVDPC 494
           +PFVPD++           W+   TET+A D R++ F PG +WH F+  + S Y   DP 
Sbjct: 495 EPFVPDRVPSPEGGETMVAWEDLPTETIAADPRYWEFTPGARWHGFKHVSRSGYAMTDPN 554

Query: 495 KLLLTTPGIDTASGNYSDFGIPATILANYLRENGIVPEKCDLNSILFLLTPAEDIAKMQH 554
           KL L TPG +  +G Y+++GIPA ++A YLREN +VPEK DLNS+LFLLTP  + +K   
Sbjct: 555 KLTLITPGFNRDTGAYAEYGIPAPVVAQYLRENRVVPEKNDLNSMLFLLTPGVESSKAGT 614

Query: 555 LVALIARFEKHIEQDSLLSEVLPAVYKSNEQRYKNYTLRQLCQEMHDLYVSYDVKELQKE 614
           L++ +  F++  + ++LL + +P   +   QRY+   ++ LC EMH  +   +V  LQ+ 
Sbjct: 615 LLSSLVAFKRRHDDNALLDDAIPEFVRRRPQRYRGLRIQDLCAEMHAFFRDRNVSTLQRA 674

Query: 615 MFRKNYFPRIAMNPQDANTEFVRGNIELVSLAKAEGRIAAEGALPYPPGVLCVVPGEIWG 674
            F   + P + M P DA     R  ++ + + + +GRIA    + YPPG+  ++PGE   
Sbjct: 675 QFSPEHRPHMVMRPNDAVRMLTRNQVDYLPIDQIDGRIATTLWVVYPPGIATIIPGERLC 734

Query: 675 GAAQ---RYFLALEEGINLLPGFAPELQGVYIQQDEDGWNRAYGYV 717
             A+    Y    E   NL PGF  E+QG+Y + + DG  R Y YV
Sbjct: 735 ERARPMLDYLKMFERSANLFPGFEAEIQGLYREIEPDGSIRFYTYV 780


Lambda     K      H
   0.321    0.138    0.420 

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: 1422
Number of extensions: 49
Number of successful extensions: 6
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: 720
Length of database: 783
Length adjustment: 40
Effective length of query: 680
Effective length of database: 743
Effective search space:   505240
Effective search space used:   505240
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 (21.9 bits)
S2: 55 (25.8 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