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

GapMind for catabolism of small carbon sources

Aligments 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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, the paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources