GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3607411 Dshi_0825 AMP-dependent synthetase
           and ligase (RefSeq)
          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 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