Alignments for a candidate for put1 in Azospirillum lipoferum B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Azospirillum lipoferum B510

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_012977293.1 AZL_RS25435 sarcosine oxidase subunit alpha

Query= BRENDA::Q76M76
         (483 letters)



>NCBI__GCF_000010725.1:WP_012977293.1
          Length = 1000

 Score =  145 bits (365), Expect = 8e-39
 Identities = 138/490 (28%), Positives = 205/490 (41%), Gaps = 87/490 (17%)

Query: 15  RGRKVTIHFEGQPVEAYEGETIAMALHAAGIRVLSHSAEKHRPRGLFCAIGKCSSCLVKV 74
           RGR+V   F+G      EG+T+A AL A G+ ++  S + HRPRG+  A  +  + LV  
Sbjct: 14  RGRQVRFSFDGVDYTGCEGDTLASALLANGVHLVGRSFKYHRPRGILTAGSEEPNALVGS 73

Query: 75  NG-----VPNVRSCITLVEEGMKVEMQRGKETLPKG------------------------ 105
           N       PN R+ +  V EG+K E Q    +L +                         
Sbjct: 74  NRGNGRFEPNTRATVLEVFEGLKTESQNRWPSLTRDIGAVNDALYRLFSAGFYYKTFMWP 133

Query: 106 ------------------AKPPAWKDAPRYKA-----DVVVIGGGPAGLMAAIHAADAGA 142
                              K P   D   Y +     DV+V+GGG AGL AA+ A   GA
Sbjct: 134 RSFWDKLYEPVIRNAAGLGKAPTAPDPDSYASRFAHCDVLVVGGGAAGLAAALEAGRGGA 193

Query: 143 SVILIDENPMLGGQLVKQTHKFFGKREQFAGVRGVKIAEILGEEVKKRGNIEVFLETSAV 202
           SVIL DE   LGG L+ +         +  G       E     +    N+ V   T+A+
Sbjct: 194 SVILCDEQNELGGSLLSEP------AAEINGQLAWDWLEDTNAALAAMPNVTVLPRTTAI 247

Query: 203 GVFHEGEEKLVAAVRKN----------KELLEFLGKTLVVATGAMEKMIPFENNDLPGIY 252
           G +H+    L   +  +          + + +   K +V+A GA+EK + F  ND PG+ 
Sbjct: 248 GYYHQNFVGLCQRLTDHLAIVPDGAPRERMWKVRAKRVVLAQGALEKPLVFAGNDRPGVM 307

Query: 253 GAGAIQTLMNTYGVKPGDRVLIVGAGNVGLILAYQLIQAGVEVKAIVEAMPKVGGYFVHA 312
            AGA +T +N YGVK G+RV++V + +     A+ L +AGVEV AIV+    V      A
Sbjct: 308 LAGAARTYLNRYGVKVGNRVVVVTSHDSAWHAAFDLAKAGVEVAAIVDIRGSVPSQLAAA 367

Query: 313 AKVRRLGVPILTRHTILRAEGKDRVERAVIAQLDENWRPVPGTEKVFEVDTIALAVGLRP 372
           A   R  +  L   T+   +G+ R+    +  +      V G E +   D + ++ G  P
Sbjct: 368 ADALR--IKTLIGWTVSDTKGRLRISSVRVNPVTGG--KVGGAETI-ACDALLMSGGWTP 422

Query: 373 SIELLHQAGCQVKFVRE----LSGHVAVRDGRMETTVQGIFVAGDSAGIEEATTAMLEGK 428
           S+ L       + +  +    L GH     G+ E       +AG   G      A  +G 
Sbjct: 423 SVHLFSHTQGSLTWNEDGQMFLPGH-----GKEECR-----LAGAGMGRFGLKAAFEDGA 472

Query: 429 IAGIAAALKA 438
            AG AAA  A
Sbjct: 473 AAGAAAAAAA 482


Lambda     K      H
   0.319    0.138    0.397 

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: 1062
Number of extensions: 54
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 483
Length of database: 1000
Length adjustment: 39
Effective length of query: 444
Effective length of database: 961
Effective search space:   426684
Effective search space used:   426684
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources