GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puo in Klebsiella michiganensis M5al

Align Primary amine oxidase 1; AtAO1; EC 1.4.3.21 (characterized)
to candidate BWI76_RS13080 BWI76_RS13080 tyramine oxidase

Query= SwissProt::O23349
         (650 letters)



>FitnessBrowser__Koxy:BWI76_RS13080
          Length = 752

 Score =  264 bits (675), Expect = 1e-74
 Identities = 197/654 (30%), Positives = 301/654 (46%), Gaps = 52/654 (7%)

Query: 23  HPLDPLTPQEINKTSFIVKKSHLGNLKDLT-FHYLDLEEPNKSHVLQW-LSPNPSKKPPP 80
           HPL+ L+  EI+    IVK +   + K  T F  + L EP+K  V  + L+  P   P  
Sbjct: 121 HPLNSLSAAEISAAVAIVKAA--ADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAP-- 176

Query: 81  PRRRSFVVVRAGGQTYELIIDLTTSKIAS-SRIYTGHGF---PSFTFIELFKASKLPLTY 136
             R + V++  G    E ++DL   K+ S + I   HG      F  ++    +      
Sbjct: 177 --RTADVIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAE 234

Query: 137 PPFKKSILDRSLNISEVSCIPFTVGWY----GETTTRRELKASCFYRDGSVNVFTRPIEG 192
              K  I D S    +V   P TVG++    G     R LK   +   G  N +  PIE 
Sbjct: 235 VLKKHGIDDPS----KVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIEN 290

Query: 193 ITVTIDVDSMQVIKYSDRFRKPIPDKEGNDFRTKHRPFPF-----FCNVSDTGFKILGNR 247
           +   +D++  ++IK  +    P+P      +  + R  P              + I G+ 
Sbjct: 291 LVAVVDLEQKKIIKIEEGPTIPVP-MAARPYDGRDRVAPTVKPLEIIEPEGKNYTITGDM 349

Query: 248 VKWANWKFHVGFTARAGVTISTASVLDPRTKRFRRVMYRGHVSETFVPYMDPTYEWYYRT 307
           + W NW FH+   +R G  +ST +  D   KR  +VMY G +    VPY DP   WY++ 
Sbjct: 350 IHWRNWDFHLRMNSRVGPILSTVTWNDNGKKR--QVMYEGSLGGMIVPYGDPDVGWYFKA 407

Query: 308 FMDIGEFGFGRSAVNLQPLIDCPQNAAFLDGHVAGPDGTAQKMTNVMCVFEKNGYGASFR 367
           ++D G++G G     +    D P NA  LD  +A   GT   +   + +FE+   G  ++
Sbjct: 408 YLDSGDYGMGTLTSPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYA-GPEYK 466

Query: 368 HTEINVPGQVITSGEAEISLVVRMVATLGNYDYIVDWEFKKNGAIRVGVDLTGVLEVKAT 427
           H E+  P       E    LVVR ++T+GNYDYI DW F +NG I +    TG+  VK  
Sbjct: 467 HLEMGKPNVSTERRE----LVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGV 522

Query: 428 -SYTSNDQIT--ENVYGTLVAKNTIAVNHDHYLTYYLDLDVDGNGNSLVKAKLKTVRVTE 484
            + T +D     +  YGTL+  N +   H H   + LDLDVDG  N+LV    +    T 
Sbjct: 523 QAKTMHDPSAKEDTRYGTLIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTA 582

Query: 485 VN-KTSSRRKSYWTVVKE--TAKTEADGRVRLGSDPVELLIVNPNKKTKIGNTVGYRLIP 541
              +TS+ + + +T+  E   A+    G +RL S        N  K+ ++GN V Y++IP
Sbjct: 583 GGPRTSTMQINQYTIASEQKAAQKFDPGTIRLLS--------NTTKENRMGNPVSYQIIP 634

Query: 542 ----EHLQATSL-LTDDDYPELRAGYTKYPVWVTAYDRSERWAGGFYSDRSRGDDGLAVW 596
                H  AT      D++   R  +    +WVT Y  +ER+  G Y +RS  D GL  +
Sbjct: 635 YAGGTHPVATGAKFAPDEWIYHRLSFMDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQY 694

Query: 597 SSRNREIENKDIVMWYNVGFHHIPYQEDFPVMPTLHGGFTLRPSNFFDNDPLIG 650
           +  +  ++N D V+W   G  H+   E++P+MPT      L+P NFFD  P +G
Sbjct: 695 AKDDESLDNHDDVVWITTGTTHVARAEEWPIMPTEWAHALLKPWNFFDETPTLG 748


Lambda     K      H
   0.320    0.138    0.424 

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: 1260
Number of extensions: 58
Number of successful extensions: 8
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: 650
Length of database: 752
Length adjustment: 39
Effective length of query: 611
Effective length of database: 713
Effective search space:   435643
Effective search space used:   435643
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 (21.8 bits)
S2: 54 (25.4 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