GapMind for catabolism of small carbon sources

 

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

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011384701.1 AMB_RS11645 propionyl-CoA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>NCBI__GCF_000009985.1:WP_011384701.1
          Length = 638

 Score =  708 bits (1828), Expect = 0.0
 Identities = 338/623 (54%), Positives = 447/623 (71%), Gaps = 2/623 (0%)

Query: 58  YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117
           Y+  +  S+ DPE FWG+AA++I WYK W K L++   P   WFV    N CYNA+DRH+
Sbjct: 5   YQQAYEKSLKDPEGFWGEAAKEIHWYKTWDKVLDDSKKPFYRWFVGAETNTCYNAVDRHV 64

Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177
           E G+G + AIIYDSPVT TK  ISY E+ +QVS+LAG +   GV KGD V++YMPM+P+A
Sbjct: 65  EQGRGAQTAIIYDSPVTSTKRKISYDELKDQVSRLAGAMAALGVAKGDRVLLYMPMVPEA 124

Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237
           +  MLA AR+GAIHS++FGGFA  EL+TRI+  KPKV+++AS GIE  R + Y P+L+EA
Sbjct: 125 VVGMLAVARLGAIHSVVFGGFAPAELATRINDAKPKVILSASCGIEGSRVIAYKPMLDEA 184

Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSG 297
           + + +HKP   ++  RP    V   +G DLDW E  AKA+  DCVPVL+  PLYILYTSG
Sbjct: 185 IALSEHKPGHTIMLQRPQSVAVMDKAG-DLDWTEVCAKAKPADCVPVLATDPLYILYTSG 243

Query: 298 TTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNT 357
           TTG PKGVVR  GG+ V L W+M  +Y +KPGEV+WAASD+GWVVGHSYICY PLL+G+T
Sbjct: 244 TTGQPKGVVRDNGGHMVALMWSMKYVYDIKPGEVFWAASDVGWVVGHSYICYAPLLNGST 303

Query: 358 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 417
           TV+YEGKPVGTPDAGA++R+++E+ +A+LFTAPTA RAI+++DP   L K+Y LT F+ L
Sbjct: 304 TVVYEGKPVGTPDAGAFWRMISEYKMASLFTAPTAFRAIKREDPNGELLKKYDLTGFRAL 363

Query: 418 FVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPG 477
           F+AGER D +T+ W+++  +VPV+DHWWQTETG  I A+C+GL +     PG   K VPG
Sbjct: 364 FLAGERSDPDTINWAREKLKVPVVDHWWQTETGWAIAANCLGL-HEFPIKPGSPTKPVPG 422

Query: 478 YNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 537
           + + +LD+  Q  +A  +G++VV+LPLPPGA   LW   +     Y+ +FPG Y T DAG
Sbjct: 423 WGLEVLDEGHQPCEAGKVGSLVVRLPLPPGALLTLWNADQRCIDSYYSEFPGCYKTADAG 482

Query: 538 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLAL 597
            +DE+GY Y+MSR DD+INVAGHR+S G +EE + SH  V +CAV+G  D LKG +PL  
Sbjct: 483 MIDEDGYAYIMSRTDDIINVAGHRLSTGGMEEVLASHPDVAECAVIGVADQLKGQLPLGF 542

Query: 598 CVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNG 657
             LK  V    +QV+ E+VK VR+ IGPVAAF+    V +LPKTRSGKI R T+  + + 
Sbjct: 543 ICLKAGVTKPHDQVIAEVVKLVREKIGPVAAFKTCTVVNRLPKTRSGKILRGTMQKIADN 602

Query: 658 KPYKVTPTIEDPSIFGHIEEVLK 680
           + +K+  TI+DPSI   I E L+
Sbjct: 603 QDFKMPATIDDPSILDEIGESLE 625


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: 1339
Number of extensions: 61
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: 638
Length adjustment: 38
Effective length of query: 645
Effective length of database: 600
Effective search space:   387000
Effective search space used:   387000
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