GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Dinoroseobacter shibae DFL-12

Align Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate 3607411 Dshi_0825 AMP-dependent synthetase and ligase (RefSeq)

Query= SwissProt::Q9H6R3
         (686 letters)



>FitnessBrowser__Dino:3607411
          Length = 630

 Score =  694 bits (1790), Expect = 0.0
 Identities = 328/622 (52%), Positives = 435/622 (69%), Gaps = 2/622 (0%)

Query: 62  YKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHI 121
           Y   +AA   DPE FW +AA+ I W  P    L + ++P   WF +  +N C+NAVDRH+
Sbjct: 3   YSQTYAAWKNDPEGFWMEAAQAIDWVTPPGAALNSDNAPLYEWFTDAEVNTCFNAVDRHV 62

Query: 122 ENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQA 181
           + G GD++AII+DSPVT+TK   TY E+ E+VS LAG L   GI+KGD V+IYMPM+PQA
Sbjct: 63  QAGNGDRVAIIHDSPVTHTKQEITYAELQERVSLLAGALRAKGIEKGDRVLIYMPMVPQA 122

Query: 182 MYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEA 241
           +  MLACAR+GAIHS++FGGFA+ EL+ RID   PK ++ AS GIEPGR V Y PL++ A
Sbjct: 123 LEAMLACARLGAIHSVVFGGFAANELAVRIDDATPKAIIAASCGIEPGRVVHYKPLLDGA 182

Query: 242 LKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSG 301
           + +  HKPD  LI+ R   E   L PGRD DW E        +CVPV   HP YILYTSG
Sbjct: 183 IDLATHKPDFCLIFQR-EQEVAHLEPGRDFDWHEAQYGVDPAECVPVAGNHPAYILYTSG 241

Query: 302 TTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNT 361
           TTG PKGV+RPT G+ V L+W+M +IY + PG+V+WAASD+GWVVGHSYICY PL+HGNT
Sbjct: 242 TTGQPKGVLRPTAGHLVALNWTMKNIYNVDPGDVFWAASDVGWVVGHSYICYAPLIHGNT 301

Query: 362 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 421
           T+++EGKPVGTPDAG ++RV++EH V + FTAPTA+RA++++DP      +Y L+  KT+
Sbjct: 302 TIVFEGKPVGTPDAGTFWRVISEHKVKSFFTAPTALRAVKREDPNGEFIGKYDLSHLKTV 361

Query: 422 FVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVPG 481
           ++AGER D +T++W+ +   VPV+DHWWQTETG  I A+ +G+ +      G    ++PG
Sbjct: 362 YLAGERADPDTIQWTMDKLGVPVIDHWWQTETGWAIAANPMGIEHLPV-KIGSPSVAMPG 420

Query: 482 YNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 541
           Y+V +LD+    +    LG I VKLPL PG    LW+ +E F   Y   FPGYY+T DAG
Sbjct: 421 YDVQVLDEGGHPVAPGTLGAIAVKLPLAPGTLPNLWQAEERFVKSYLTTFPGYYETGDAG 480

Query: 542 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLAL 601
           Y+DE+GYLY+M+R DDVINVAGHR+S GA+EE + SH  VA+CAV+G  D LKG +PL  
Sbjct: 481 YIDEDGYLYIMARTDDVINVAGHRLSTGAMEEVLASHPDVAECAVIGVSDTLKGQMPLGF 540

Query: 602 CVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVNG 661
             L   +N   +++ +E VK VR+ IGPVAAF+ A  V +LPKTRSGKI R  +  I +G
Sbjct: 541 LCLSAGVNRPHDEIAKECVKLVREKIGPVAAFKLACVVDRLPKTRSGKILRGTMVNIADG 600

Query: 662 KPYKITSTIEDPSIFGHVEEML 683
            P+K+ +TI+DP+I   + E L
Sbjct: 601 TPWKMPATIDDPAILDEITEAL 622


Lambda     K      H
   0.318    0.136    0.422 

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: 1388
Number of extensions: 68
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: 686
Length of database: 630
Length adjustment: 38
Effective length of query: 648
Effective length of database: 592
Effective search space:   383616
Effective search space used:   383616
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