GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Shewanella amazonensis SB2B

Align Propionate--CoA ligase (EC 6.2.1.17) (characterized)
to candidate 6937194 Sama_1364 acyl-coenzyme A synthetase/AMP-(fatty) acid ligase (RefSeq)

Query= reanno::Phaeo:GFF1175
         (629 letters)



>FitnessBrowser__SB2B:6937194
          Length = 644

 Score =  777 bits (2007), Expect = 0.0
 Identities = 367/615 (59%), Positives = 452/615 (73%)

Query: 13  NPEQFWMEAAEAISWDSAPTKALTDKGDGLYEWFADARVNTCYNAVDRHVEQGRGEQTAI 72
           NPEQ+W +AA+ + W  AP+  L      LY W+ D  +NTCYNA+DR V+ GRG QTA 
Sbjct: 25  NPEQYWRKAADMVDWHKAPSTILDSSQAPLYRWYTDGEINTCYNALDRQVDAGRGSQTAF 84

Query: 73  IYDSPITHTKREISYVELRNRVATLAGALRAKGVEKGDRVIIYMPMIPEALEAMLACARL 132
            Y SP+T T+  ISY E   +V  LAG L+A+GV KGDRV+IYMPM+PE   AMLACAR+
Sbjct: 85  HYVSPVTETEYSISYTECLAQVKRLAGLLKAQGVNKGDRVVIYMPMVPETAYAMLACARI 144

Query: 133 GAVHSVVFGGFAANELAVRIDDATPKAIIAASCGLEPGRTVHYKPLLDGAIDLATHKPDF 192
           GA+HSVVFGGFAANELA RI+DA P  +++ASCG+EP   V YKPLLD A+  A+HK   
Sbjct: 145 GAIHSVVFGGFAANELASRINDAKPVMVLSASCGVEPSGVVAYKPLLDAALAQASHKVSK 204

Query: 193 CVIFQREQEVAELIEGRDVNWHGFQYGVEPAECVPVEGNHPAYILYTSGTTGQPKGVIRH 252
           C+I QR Q  A +  GRD++W         A+ VPV+   P Y+LYTSGTTGQPKGV+R 
Sbjct: 205 CLILQRPQYEAAMTPGRDLDWQESVASAADADWVPVKATDPLYVLYTSGTTGQPKGVVRD 264

Query: 253 TAGQLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYGPLIHGNTTIVFEGKPIGT 312
             G  VAL W+M+ +Y+++PGD FWAASDVGWVVGHSYI YGPLI G T++++EGKP+GT
Sbjct: 265 NGGHAVALAWSMRYLYDIEPGDTFWAASDVGWVVGHSYIVYGPLIAGATSVLYEGKPVGT 324

Query: 313 PDAGTFWRVISEHKVKSFFTAPTAFRAVKREDPKGEFVKKYDLSCLKQVYLAGERADPDT 372
           PDAG FWR I ++ VKSFFTAPTA RA+KREDP+G F +  +L CLKQ++LAGER DPDT
Sbjct: 325 PDAGAFWRTIKKYGVKSFFTAPTAIRAIKREDPEGFFCRNTNLDCLKQMFLAGERCDPDT 384

Query: 373 ITWAQEQLKVPVIDHWWQTETGWSIAANPLGIEELPTKLGSPAVPMPGYTVDILDEGGHP 432
           + WAQE L  PVIDHWWQTETGW +A+N +GI ++P K GSPA P+PGY VD++DE G+ 
Sbjct: 385 LLWAQEMLGKPVIDHWWQTETGWPVASNLMGIAQMPIKPGSPARPVPGYQVDVVDEAGNS 444

Query: 433 VAPGELGAIAVKLPLPPGTLPTLWNAEDRFKKSYLTTFPGYYETGDAGMKDEDGYLYIMA 492
           V  GE G + ++LPLPPGTLPTLW  + R+  SYL+ +P  Y TGDAG  DEDGYLYIM+
Sbjct: 445 VGAGEYGNVVIRLPLPPGTLPTLWQNDKRYIDSYLSMYPDCYLTGDAGYMDEDGYLYIMS 504

Query: 493 RTDDVINVAGHRLSTGAMEEVLAGHPDVAECAVIGVSDSLKGQAPVGFLCLNAGCDTPHE 552
           R DDVINVAGHRLSTG  EEVL  HP VAE AVIGV D LKGQ P+G + L  G D   E
Sbjct: 505 RIDDVINVAGHRLSTGRFEEVLCQHPAVAEAAVIGVEDKLKGQVPLGLVVLKNGVDITDE 564

Query: 553 DVVAQVVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADGTDWKMPATIDDP 612
            +  ++V LVR +IGPVAAFKL   + +LPKTRSGKILR TM  IAD  ++ +PATI+DP
Sbjct: 565 QLNKELVALVRSEIGPVAAFKLVSAIPKLPKTRSGKILRATMRKIADNQEYSVPATIEDP 624

Query: 613 AILDEITTALQGLGY 627
           A L+ +   L  +GY
Sbjct: 625 ATLELVRNTLTRMGY 639


Lambda     K      H
   0.318    0.137    0.428 

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: 1344
Number of extensions: 65
Number of successful extensions: 2
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: 629
Length of database: 644
Length adjustment: 38
Effective length of query: 591
Effective length of database: 606
Effective search space:   358146
Effective search space used:   358146
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 Aug 03 2021. The underlying query database was built on Aug 03 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