GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Shewanella amazonensis SB2B

Align putrescine-pyruvate transaminase (EC 2.6.1.113) (characterized)
to candidate 6938540 Sama_2643 putative aminotransferase (RefSeq)

Query= BRENDA::Q9I6J2
         (456 letters)



>FitnessBrowser__SB2B:6938540
          Length = 460

 Score =  593 bits (1529), Expect = e-174
 Identities = 289/445 (64%), Positives = 342/445 (76%), Gaps = 2/445 (0%)

Query: 14  QALSRDHHLPPFTDYKQLNEKGARIITKAEGVYIWDSEGNKILDAMAGLWCVNVGYGREE 73
           QA+   HHL PFTD   L ++G R+I +AEGVYIWD++GNK+LDAMAGLWCVNVGYGR+ 
Sbjct: 13  QAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKS 72

Query: 74  LVQAATRQMRELPFYNLFFQTAHPPVVELAKAIADVAPEGMNHVFFTGSGSEANDTVLRM 133
           +  AA  Q++ LPFYN FFQ  H P + LA  IA +AP  MN VFFTGSGSEANDT LRM
Sbjct: 73  IADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRM 132

Query: 134 VRHYWATKGQPQKKVVIGRWNGYHGSTVAGVSLGGMKALHEQGDFPIPGIVHIAQPYWYG 193
           VR YW  KG P KK +I R N YHGSTVAG SLGGM  +H+QGD PIPGIVHI QPYW+G
Sbjct: 133 VRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPYWFG 192

Query: 194 EGGDMSPDEFGVWAAEQLEKKILEVGEENVAAFIAEPIQGAGGVIVPPDTYWPKIREILA 253
           EG DMSP+ FG+  A+ LE KILE+GE+ VAAFIAEP QGAGGVI+PPD+YW +I+ IL 
Sbjct: 193 EGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILE 252

Query: 254 KYDILFIADEVICGFGRTGEWFGSQYYGNAPDLMPIAKGLTSGYIPMGGVVVRDEIVEVL 313
           KY+ILFI DEVI GFGRTG WF +Q  G  PDL+ IAKG+TSGYIPMGGV+V D + +VL
Sbjct: 253 KYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVL 312

Query: 314 -NQGGEFYHGFTYSGHPVAAAVALENIRILREEKIIEKVKAETAPYLQKRWQELADHPLV 372
            + GGEF HGFTYSGHPVAAAVALENIRIL EE++++KV+ +T PYLQ R Q L+ HPLV
Sbjct: 313 ISDGGEFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPLV 372

Query: 373 GEARGVGMVAALELVKNKKTRERF-TDKGVGMLCREHCFRNGLIMRAVGDTMIISPPLVI 431
           GE RG+GMV A+ELV +K +  RF ++   GMLCRE C  +GL+MRAVGDTMIISPPL I
Sbjct: 373 GEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMIISPPLCI 432

Query: 432 DPSQIDELITLARKCLDQTAAAVLA 456
              +IDELI  A + L  T   + A
Sbjct: 433 TRDEIDELIFKASQALSLTLEKIAA 457


Lambda     K      H
   0.320    0.138    0.425 

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: 692
Number of extensions: 24
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: 456
Length of database: 460
Length adjustment: 33
Effective length of query: 423
Effective length of database: 427
Effective search space:   180621
Effective search space used:   180621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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