GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella sp. ANA-3

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate 7024497 Shewana3_1675 AMP-dependent synthetase and ligase (RefSeq)

Query= BRENDA::A0A0G2K047
         (683 letters)



>FitnessBrowser__ANA3:7024497
          Length = 640

 Score =  666 bits (1718), Expect = 0.0
 Identities = 326/631 (51%), Positives = 438/631 (69%), Gaps = 6/631 (0%)

Query: 49  LTTSSGGGEYKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNI 108
           L T +G   ++T    S+A+ + FW +AA+ + W  P  + L+    P   WF +G LN 
Sbjct: 5   LMTDAGQQLHQT----SIANKQAFWQQAAKALDWVTPSKQILDESEAPFYHWFSDGELNT 60

Query: 109 CYNAIDRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVV 168
           CYNA+DRH+  G+G++IAI Y SPVT+T+ +I+Y+E+  QV++LAG L   GV KGD VV
Sbjct: 61  CYNAVDRHVLAGRGEQIAIHYVSPVTETEYSITYRELQAQVARLAGYLQSVGVAKGDRVV 120

Query: 169 IYMPMIPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKV 228
           IYMPM+P+  YAMLACARIGAIHS++FGGFA+ EL+TRI+  KPK+V++AS GIEP   V
Sbjct: 121 IYMPMVPETAYAMLACARIGAIHSVVFGGFAANELATRINDAKPKLVMSASCGIEPSGVV 180

Query: 229 EYMPLLEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEH 288
            Y PLL++AL    HK +  LI NRP  E   + +GRD DW+  +  + S DCV V +  
Sbjct: 181 PYKPLLDKALNEAVHKVEHCLILNRPQYE-AQMQAGRDKDWQTALCTSDSADCVTVKATD 239

Query: 289 PLYILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYIC 348
           PLY+LYTSGTTG PKGVVR  GG+AV L W+M++IY +  G+V+WAASD+GWVVGHSYI 
Sbjct: 240 PLYVLYTSGTTGQPKGVVRDNGGHAVALAWSMANIYDIAQGDVFWAASDVGWVVGHSYIV 299

Query: 349 YGPLLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQ 408
           YGPLL G TT+LYEGKPVGTPD GA++R +A++ V + FTAPTAIRAI+++DP       
Sbjct: 300 YGPLLVGATTLLYEGKPVGTPDPGAFWRTIAKYRVKSFFTAPTAIRAIKREDPDGEFILG 359

Query: 409 YSLTRFKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPP 468
             L+  K +F+AGERCD +TL W++     PV+DHWWQTETG P+ A+ +G+        
Sbjct: 360 VDLSCLKNVFLAGERCDPDTLHWAEAKLHKPVIDHWWQTETGWPVAANLMGVAPIAV-KA 418

Query: 469 GQAGKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFP 528
           G  G+ VPGY V ++D+   K+ A   GN+V+KLPLPPG  + LW+N + ++  Y   +P
Sbjct: 419 GSPGRPVPGYEVDVVDELGAKVAANVSGNVVIKLPLPPGTLTTLWQNNKRYQDSYLSMYP 478

Query: 529 GYYDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDP 588
           GYY T DAGYMDE+GYLY+MSR+DD+INVAGHR+S G  EE +  H  V + AV+G +D 
Sbjct: 479 GYYLTGDAGYMDEDGYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHPDVAEAAVIGVDDK 538

Query: 589 LKGHVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPR 648
           LKG VPL L VLKK V  T+E++ ++++  VRQ IGPVA+FR    +++LPKTRSGKI R
Sbjct: 539 LKGQVPLGLVVLKKGVTITDEELHKQLIALVRQEIGPVASFRLVSAIQKLPKTRSGKILR 598

Query: 649 STLSALVNGKPYKVTPTIEDPSIFGHIEEVL 679
            T+  + + + Y    TIEDP     +   L
Sbjct: 599 GTMRKIADNQQYTAPATIEDPQTLDLVRTTL 629


Lambda     K      H
   0.318    0.136    0.421 

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: 1235
Number of extensions: 52
Number of successful extensions: 3
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: 683
Length of database: 640
Length adjustment: 38
Effective length of query: 645
Effective length of database: 602
Effective search space:   388290
Effective search space used:   388290
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: 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